Papers Citing VMD

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1818 citations, list generated March 21, 2007.

Imai, T., Hiraoka, R., Kovalenko, A., Hirata, F.
Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 66:804-813, MAR 2007
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Pantano, S., Carafoli, E.
The role of phosphorylation on the structure and dynamics of phospholamban: A model from molecular simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 66:930-940, MAR 2007
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Tynan, F.E., Reid, H.H., Kjer-Nielsen, L., Miles, J.J., Wilce, M.C.J., Kostenko, L., Borg, N.A., Williamson, N.A., Beddoe, T., Purcell, A.W., Burrows, S.R., McCluskey, J., Rossjohn, J.
A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule
NATURE IMMUNOLOGY, 8:268-276, MAR 2007
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Waheed, N., Mattice, W.L., von Meerwall, E.D.
Enhanced diffusion at intermediate stereochemical composition in polypropylene by dynamical Monte Carlo
MACROMOLECULES, 40:1504-1511, MAR 6 2007
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Tomsic, M., Jamnik, A., Fritz-Popovski, G., Glatter, O., Vlcek, L.
Structural properties of pure simple alcohols from ethanol, propanol, butanol, pentanol, to hexanol: Comparing Monte Carlo simulations with experimental SAXS data
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1738-1751, FEB 22 2007
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Roe, D.R., Okur, A., Wickstrom, L., Hornak, V., Simmerling, C.
Secondary structure bias in generalized born solvent models: Comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1846-1857, FEB 22 2007
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Melquiond, A., Gelly, J.C., Mousseau, N., Derreumaux, P.
Probing amyloid fibril formation of the NFGAIL peptide by computer simulations
JOURNAL OF CHEMICAL PHYSICS, 126: Art. No. 065101, FEB 14 2007
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Malek, K., Jansen, A.P.J., Li, C., van Santen, R.A.
Enantioselectivity of immobilized Mn-salen complexes: A computational study
JOURNAL OF CATALYSIS, 246:127-135, FEB 15 2007
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Cojocaru, V., Winn, P.J., Wade, R.C.
The ins and outs of cytochrome P450s
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1770:390-401, MAR 2007
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Lee, H.J., Diavatis, T., Tennakoon, S., Yu, P.L., Gao, X.L.
Solution structure of DNA/RNA hybrid duplex with C8-propynyl 2 '-deoxyadenosine modifications: Implication of RNase H and DNA/RNA duplex interaction
BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION, 1769:20-28, JAN 2007
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Amaro, R.E., Sethi, A., Myers, R.S., Davisson, V.J., Luthey-Schulten, Z.A.
A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase
BIOCHEMISTRY, 46:2156-2173, FEB 27 2007
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Olsen, S., Smith, S.C.
Radiationless decay of red fluorescent protein chromophore models via twisted intramolecular charge-transfer states
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:2054-2065, FEB 21 2007
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Oelschlaeger, P., Pleiss, J.
Hydroxyl groups in the beta beta sandwich of metallo-beta-lactamases favor enzyme activity: Tyr218 and Ser262 pull down the lid
JOURNAL OF MOLECULAR BIOLOGY, 366:316-329, FEB 9 2007
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Isgro, T.A., Schulten, K.
Association of nuclear pore FG-repeat domains to NTF2 import and export complexes
JOURNAL OF MOLECULAR BIOLOGY, 366:330-345, FEB 9 2007
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Oelschlaeger, P., Klahn, M., Beard, W.A., Wilson, S.H., Warshel, A.
Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: Improved accuracy in studies of structural features and mutational effects
JOURNAL OF MOLECULAR BIOLOGY, 366:687-701, FEB 16 2007
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Gorfe, A.A., Hanzal-Bayer, M., Abankwa, D., Hancock, J.F., McCammon, J.A.
Structure and dynamics of the full-length lipid-modified H-ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer
JOURNAL OF MEDICINAL CHEMISTRY, 50:674-684, FEB 22 2007
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Morikis, D., Rizos, A.K., Spandidos, D.A., Krambovitis, E.
Electrostatic modeling of peptides derived from the V3-loop of HIV-1 gp120: Implications of the interaction with chemokine receptor CCR5
INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE, 19:343-351, MAR 2007
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Liu, H.L., Chen, X.Y., Focia, P.J., He, X.L.
Structural basis for stem cell factor-KIT signaling and activation of class III receptor tyrosine kinases
EMBO JOURNAL, 26:891-901, FEB 7 2007
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Choe, S.H., Sun, S.X.
Bending elasticity of anti-parallel beta-sheets
BIOPHYSICAL JOURNAL, 92:1204-1214, FEB 15 2007
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Rizzuti, B., Sportelli, L., Guzzi, R.
Structural, dynamical and functional aspects of the inner motions in the blue copper protein azurin
BIOPHYSICAL CHEMISTRY, 125:532-539, FEB 2007
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Celik, L., Lund, J.D.D., Schiott, B.
Conformational dynamics of the estrogen receptor alpha: Molecular dynamics simulations of the influence of binding site structure on protein dynamics
BIOCHEMISTRY, 46:1743-1758, FEB 20 2007
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Kuznicki, T., Masliyah, J.H., Bhattacharjee, S.
Stability and disintegration of ultrathin heptane films in water: Molecular dynamics simulations
LANGMUIR, 23:1792-1803, FEB 13 2007
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Redecke, L., von Bergen, M., Clos, J., Konarev, P.V., Svergun, D.I., Fittschen, U.E.A., Broekaert, J.A.C., Bruns, O., Georgieva, D., Mandelkow, E., Genov, N., Betzel, C.
Structural characterization of beta-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro
JOURNAL OF STRUCTURAL BIOLOGY, 157:308-320, FEB 2007
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Zhang, J.F., Rivero, M., Choi, S.K.
Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates
JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS, 40:545-553, FEB 14 2007
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Berrera, M., Pantano, S., Carloni, P.
Catabolite activator protein in aqueous solution: A molecular simulation study
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1496-1501, FEB 15 2007
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Khafizov, K., Anselmi, C., Menini, A., Carloni, P.
Ligand specificity of odorant receptors
JOURNAL OF MOLECULAR MODELING, 13:401-409, MAR 2007
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Liu, S.Q., Liu, S.X., Fu, Y.X.
Dynamic domains and geometrical properties of HIV-1 gp120 during conformational changes induced by CD4 binding
JOURNAL OF MOLECULAR MODELING, 13:411-424, MAR 2007
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Homeyer, N., Essigke, T., Meiselbach, H., Ullmann, G.M., Sticht, H.
Effect of HPr phosphorylation on structure, dynamics, and interactions in the course of transcriptional control
JOURNAL OF MOLECULAR MODELING, 13:431-444, MAR 2007
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Murtola, T., Kupiainen, M., Falck, E., Vattulainen, I.
Conformational analysis of lipid molecules by self-organizing maps
JOURNAL OF CHEMICAL PHYSICS, 126: Art. No. 054707, FEB 7 2007
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Mongan, J., Simmerling, C., McCammon, J.A., Case, D.A., Onufriev, A.
Generalized Born model with a simple, robust molecular volume correction
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 3:156-169, JAN-FEB 2007
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Lee, M.S., Olson, M.A.
Assessment of detection and refinement strategies for de novo protein structures using force field and statistical potentials
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 3:312-324, JAN-FEB 2007
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Lacadena, J., Alvarez-Garcia, E., Carreras-Sangra, N., Herrero-Galan, E., Alegre-Cebollada, J., Garcia-Ortega, L., Onaderra, M., Gavilanes, J.G., del Pozo, A.M.
Fungal ribotoxins: molecular dissection of a family of natural killers
FEMS MICROBIOLOGY REVIEWS, 31:212-237, MAR 2007
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Teng, W.J., Allis, D.G., Ruhlandt-Senge, K.
Synthetic, structural, and theoretical investigations of alkali metal germanium hydrides - Contact molecules and separated
CHEMISTRY-A EUROPEAN JOURNAL, 13:1309-1319, 2007
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Chen, C.Y., Beck, B.W., Krause, K., Weksberg, T.E., Pettitt, B.M.
Effects of dimerization of Serratia marcescens endonuclease on water dynamics
BIOPOLYMERS, 85:241-252, FEB 15 2007
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Tu, S.L., Rockwell, N.C., Lagarias, J.C., Fisher, A.J.
Insight into the radical mechanism of phycocyanobilin-ferredoxin oxidoreductase (PcyA) revealed by X-ray crystallography and biochemical measurements
BIOCHEMISTRY, 46:1484-1494, FEB 13 2007
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Neuberger, G., Schneider, G., Eisenhaber, F.
pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model
BIOLOGY DIRECT, , JAN 12 2007
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Koppen, S., Ohler, B., Langel, W.
Adsorption of collagen fragments on titanium oxide surfaces: A molecular dynamics study
ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS, 221:3-20, 2007
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Orlowski, S., Nowak, W.
Oxygen diffusion in minihemoglobin from Cerebratulus lacteus: a locally enhanced sampling study
THEORETICAL CHEMISTRY ACCOUNTS, 117:253-258, FEB 2007
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Godwin, A., Choi, J.W., Pedone, E., Balan, S., Jumnah, R., Shaunak, S., Brocchini, S., Zloh, M.
Molecular dynamics simulations of proteins with chemically modified disulfide bonds
THEORETICAL CHEMISTRY ACCOUNTS, 117:259-265, FEB 2007
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Tagami, K., Tsukada, M.
Simulated non-contact AFM images of an alcohol molecule in an alkanethiol self-assembled monolayer
NANOTECHNOLOGY, 18: Art. No. 084005, FEB 28 2007
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Kutteh, R., Vandenberg, J.I., Kuyucak, S.
Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1090-1098, FEB 8 2007
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Yamazaki, T., Imai, T., Hirata, F., Kovalenko, A.
Theoretical study of the cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1206-1212, FEB 8 2007
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Viswanathan, R., Dolgos, M., Hinde, R.J.
Quasiclassical trajectory study of the vibrational quenching of hydroxyl radicals through collision with O atoms
JOURNAL OF PHYSICAL CHEMISTRY A, 111:783-792, FEB 8 2007
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Nagata, T.
Automated design of protecting molecules for metal nanoparticles by combinatorial molecular simulations
JOURNAL OF ORGANOMETALLIC CHEMISTRY, 692:225-233, JAN 1 2007
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Jiang, Y., Kindt, J.T.
Simulations of edge behavior in a mixed-lipid bilayer: Fluctuation analysis
JOURNAL OF CHEMICAL PHYSICS, 126: Art. No. 045105, JAN 28 2007
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De Brevern, A.G., Etchebest, C., Benros, C., Hazout, S.
"Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence
JOURNAL OF BIOSCIENCES, 32:51-70, JAN 2007
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Watson, A.A., Brown, J., Harlos, K., Eble, J.A., Walter, T.S., O'Callaghan, C.A.
The crystal structure and mutational binding analysis of the extracellular domain of the platelet-activating receptor CLEC-2
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:3165-3172, FEB 2 2007
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Shevchenko, I., Rogalyov, A., Rozhenko, A.B., Roschenthaler, G.V.
Dissociation of the P=C ylidic bond
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 2, 254-258, JAN 2007
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Martens, E., Leyssen, A., Van Aelst, I., Fiten, P., Piccard, H., Hu, J., Descamps, F.J., Van den Steen, P.E., Proost, P., Van Damme, J., Liuzzi, G.M., Riccio, P., Polverini, E., Opdenakker, G.
A monoclonal antibody inhibits gelatinase B/MMP-9 by selective binding to part of the catalytic domain and not to the fibronectin or zinc binding domains
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1770:178-186, FEB 2007
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Sammalkorpi, M., Lazaridis, T.
Configuration of influenza hemagglutinin fusion peptide monomers and oligomers in membranes
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1768:30-38, JAN 2007
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Kino, K., Sato, M., Yoneyama, M., Kirimura, K.
Synthesis of DL-tryptophan by modified broad specificity amino acid racemase from Pseudomonas putida IFO 12996
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 73:1299-1305, JAN 2007
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Zhao, X.L., Sun, M., Zhao, J., Leyva, J.A., Zhu, H.W., Yang, W., Zeng, X., Ao, Y., Liu, Q., Liu, G.Y., Lo, W.H.Y., Jabs, E.W., Amzel, L.M., Shan, X.N., Zhang, X.
Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome
AMERICAN JOURNAL OF HUMAN GENETICS, 80:361-371, FEB 2007
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Sieker, F., Springer, S., Zacharias, M.
Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles
PROTEIN SCIENCE, 16:299-308, FEB 2007
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Videcoq, A., Han, M., Abelard, P., Pagnoux, C., Rossignol, F., Ferrando, R.
Influence of the potential range on the aggregation of colloidal particles
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 374:507-516, FEB 1 2007
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Reyes-Vivas, H., Diaz, A., Peon, J., Mendoza-Hernandez, G., Hernandez-Alcantara, G., De la Mora-De la Mora, I., Enriquez-Flores, S., Dominguez-Ramirez, L., Lopez-Velazquez, G.
Disulfide bridges in the mesophilic triosephosphate isomerase from Giardia lamblia are related to oligomerization and activity
JOURNAL OF MOLECULAR BIOLOGY, 365:752-763, JAN 19 2007
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Chiavarino, B., Crestoni, M.E., Fornarini, S., Rovira, C.
Protonated heme
CHEMISTRY-A EUROPEAN JOURNAL, 13:776-785, 2007
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Oliver, S.L., Asobayire, E., Charpilienne, A., Cohen, J., Bridger, J.C.
Complete genomic characterization and antigenic relatedness of genogroup III, genotype 2 bovine noroviruses
ARCHIVES OF VIROLOGY, 152:257-272, FEB 2007
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Crozier, P.S., Stevens, M.J., Woolf, T.B.
How a small change in retinal leads to G-protein activation: Initial events suggested by molecular dynamics calculations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 66:559-574, FEB 15 2007
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Noda, K., Nakamura, M., Nishida, R., Yoneda, Y., Yamaguchi, Y., Tamura, Y., Nakamura, H., Yasunaga, T.
Atomic model construction of protein complexes from electron micrographs and visualization of their 3D structure using a virtual reality system
JOURNAL OF PLASMA PHYSICS, 72:1037-1040, DEC 2006
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Pogorelov, T.V., Autenrieth, F., Roberts, E., Luthey-Schulten, Z.A.
Cytochrome c(2) exit strategy: Dissociation studies and evolutionary implications
JOURNAL OF PHYSICAL CHEMISTRY B, 111:618-634, JAN 25 2007
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Romero, M., Renard, P., Caignard, D.H., Atassi, G., Solans, X., Constans, P., Bailly, C., Pujol, M.D.
Synthesis and structure-activity relationships of new benzodioxinic lactones as potential anticancer drugs
JOURNAL OF MEDICINAL CHEMISTRY, 50:294-307, JAN 25 2007
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Xu, Z.T., Luo, H.H., Tieleman, D.P.
Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues
JOURNAL OF COMPUTATIONAL CHEMISTRY, 28:689-697, FEB 2007
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Sorensen, C.M., Rempel, L.A., Nelson, S.R., Francis, B.R., Perry, D.J., Lewis, R.V., Haas, A.L., Hansen, T.R.
The hinge region between two ubiquitin-like domains destabilizes recombinant ISG15 in solution
BIOCHEMISTRY, 46:772-780, JAN 23 2007
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Rogacheva, M.V., Bochenkova, A.V., Kuznetsova, S.A., Saparbaev, M.K., Nemukhin, A.V.
Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure
JOURNAL OF PHYSICAL CHEMISTRY B, 111:432-438, JAN 18 2007
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Mantz, Y.A., Gervasio, F.L., Laino, T., Parrinello, M.
Charge localization in stacked radical cation DNA base pairs and the benzene dimer studied by self-interaction corrected density-functional theory
JOURNAL OF PHYSICAL CHEMISTRY A, 111:105-112, JAN 11 2007
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Thevenard, J., Floquet, N., Ramont, L., Prost, E., Nuzillard, J.M., Dauchez, M., Yezid, H., Alix, A.J.P., Maquart, F.X., Brassart-Plasco, S.
Structural and antitumor properties of the YSNSG cyclopeptide derived from tumstatin
CHEMISTRY & BIOLOGY, 13:1307-1315, DEC 2006
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Topham, C.M., Smith, J.C.
Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: Quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form
BIOPHYSICAL JOURNAL, 92:769-786, FEB 2007
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Sotomayor, M., Vasquez, V., Perozo, E., Schulten, K.
Ion conduction through MscS as determined by electrophysiology and simulation
BIOPHYSICAL JOURNAL, 92:886-902, FEB 2007
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Esteban-Martin, S., Salgado, J.
Self-assembling of peptide/membrane complexes by atomistic molecular dynamics simulations
BIOPHYSICAL JOURNAL, 92:903-912, FEB 2007
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Gesellchen, F., Bertinetti, O., Herberg, F.W.
Analysis of posttranslational modifications exemplified using protein kinase A
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1764:1788-1800, DEC 2006
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Pinkett, H.W., Lee, A.T., Lum, P., Locher, K.P., Rees, D.C.
An inward-facing conformation of a putative metal-chelate-type ABC transporter
SCIENCE, 315:373-377, JAN 19 2007
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Reymond, C., Ouellet, J., Bisaillon, M., Perreault, J.P.
Examination of the folding pathway of the antigenomic hepatitis delta virus ribozyme reveals key interactions of the L3 loop
RNA-A PUBLICATION OF THE RNA SOCIETY, 13:44-54, JAN 2007
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Li, X.T., Lee, H.J., Wu, J., Breslow, E.
Contributions of the interdomain loop, amino terminus, and subunit interface to the ligand-facilitated dimerization of neurophysin: Crystal structures and mutation studies of bovine neurophysin-I
PROTEIN SCIENCE, 16:52-68, JAN 2007
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Bazykin, G.A., Dushoff, J., Levin, S.A., Kondrashov, A.S.
Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:19396-19401, DEC 19 2006
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Laakkonen, L., Jobson, R.W., Albert, V.A.
A new model for the evolution of carnivory in the bladderwort plant (Utricularia): Adaptive changes in cytochrorne c oxidase (COX) provide respiratory power
PLANT BIOLOGY, 8:758-764, NOV 2006
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Park, S., Ensign, D.L., Pande, V.S.
Bayesian update method for adaptive weighted sampling
PHYSICAL REVIEW E, 74: Art. No. 066703, DEC 2006
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Kalweit, M., Drikakis, D.
Collision dynamics of nanoscale Lennard-Jones clusters
PHYSICAL REVIEW B, 74: Art. No. 235415, DEC 2006
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Vernier, P.T., Ziegler, M.J., Sun, Y.H., Gundersen, M.A., Tieleman, D.P.
Nanopore-facilitated, voltage-driven phosphatidylserine translocation in lipid bilayers - in cells and in silico
PHYSICAL BIOLOGY, 3:233-247, DEC 2006
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Mulkidjanian, A.Y.
Proton translocation by the cytochrome bc(1) complexes of phototrophic bacteria: introducing the activated Q-cycle
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 6:19-34, 2007
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Ascano, M., Smith, W., Gregurick, S., Robinson, P.
Arrestin residues involved in the functional binding of arrestin to phosphorylated, photolyzed rhodopsin
MOLECULAR VISION, 12:1516-1525, DEC 5 2006
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Kanibolotsky, D.S., Ivanova, O.S., Lisnyak, V.V.
Comparison of NMR and MD N-H bond order parameters: example of HIV-1 protease
MOLECULAR SIMULATION, 32:1155-1163, DEC 15 2006
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Hatcher, E., Soudackov, A.V., Hammes-Schiffer, S.
Proton-coupled electron transfer in soybean lipoxygenase: Dynamical behavior and temperature dependence of kinetic isotope effects
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:187-196, JAN 10 2007
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Garforth, S.J., Kim, T.W., Parniak, M.A., Kool, E.T., Prasad, V.R.
Site-directed mutagenesis in the fingers subdomain of HIV-1 reverse transcriptase reveals a specific role for the beta 3-beta 4 hairpin loop in dNTP selection
JOURNAL OF MOLECULAR BIOLOGY, 365:38-49, JAN 5 2007
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Kikuzawa, Y., Nagata, T., Tahara, T., Ishii, K.
Photo- and redox-active dendritic molecules with soft, layered nanostructures
CHEMISTRY-AN ASIAN JOURNAL, 1:516-528, OCT 2006
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Jaud, S., Tobias, D.J., Falke, J.J., White, S.H.
Self-induced docking site of a deeply embedded peripheral membrane protein
BIOPHYSICAL JOURNAL, 92:517-524, JAN 2007
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Valente, L., Tiranti, V., Marsano, R.M., Malfatti, E., Fernandez-Vizarra, E., Donnini, C., Mereghetti, P., De Gioia, L., Burlina, A., Castellan, C., Comi, G.P., Savasta, S., Ferrero, I., Zeviani, M.
Infantile encephalopathy and defective mitochondrial DNA translation in patients with mutations of mitochondrial elongation factors EFG1 and EFTu
AMERICAN JOURNAL OF HUMAN GENETICS, 80:44-58, JAN 2007
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Arkhipov, A., Freddolino, P.L., Schulten, K.
Stability and dynamics of virus capsids described by coarse-grained modeling
STRUCTURE, 14:1767-1777, DEC 2006
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Deemagarn, T., Wiseman, B., Carpena, X., Ivancich, A., Fita, I., Loewen, P.C.
Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 66:219-228, JAN 2007
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Maiti, P.K., Goddard, W.A.
Solvent quality changes the structure of G8 PAMAM dendrimer, a disagreement with some experimental interpretations
JOURNAL OF PHYSICAL CHEMISTRY B, 110:25628-25632, DEC 28 2006
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Joannis, J., Jiang, Y., Yin, F.C., Kindt, J.T.
Equilibrium distributions of dipalmitoyl phosphatidylcholine and dilauroyl phosphatidylcholine in a mixed lipid bilayer: Atomistic semigrand canonical ensemble simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 110:25875-25882, DEC 28 2006
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Pal, S., Milano, G., Roccatano, D.
Synthetic polymers and biomembranes. How do they interact?: Atomistic molecular dynamics simulation study of PEO in contact with a DMPC lipid bilayer
JOURNAL OF PHYSICAL CHEMISTRY B, 110:26170-26179, DEC 28 2006
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Gepshtein, R., Leiderman, P., Huppert, D., Project, E., Nachliel, E., Gutman, M.
Proton antenna effect of the gamma-cyclodextrin outer surface, measured by excited state proton transfer
JOURNAL OF PHYSICAL CHEMISTRY B, 110:26354-26364, DEC 28 2006
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Hwang, H., Schatz, G.C., Ratner, M.A.
Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 110:26448-26460, DEC 28 2006
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Klein, C.D., Bachelier, A.
Molecular modeling and bioinformatical analysis of the antibacterial target enzyme MurA from a drug design perspective
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 20:621-628, OCT 2006
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Lany, S., Zunger, A.
Light- and bias-induced metastabilities in Cu(In,Ga)Se-2 based solar cells caused by the (V-Se-V-Cu) vacancy complex
JOURNAL OF APPLIED PHYSICS, 100: Art. No. 113725, DEC 1 2006
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Chang, T.C., Hou, J.
Molecular dynamics simulations on buckling of multiwalled carbon nanotubes under bending
JOURNAL OF APPLIED PHYSICS, 100: Art. No. 114327, DEC 1 2006
abstract, full text

Pacios, L.F., Gomez, L.
Conformational changes of the electrostatic potential of biphenyl: A theoretical study
CHEMICAL PHYSICS LETTERS, 432:414-420, DEC 11 2006
abstract, full text

Radhakrishnan, R., Arora, K., Wang, Y.L., Beard, W.A., Wilson, S.H., Schlick, T.
Regulation of DNA repair fidelity by molecular checkpoints: "Gates" in DNA polymerase beta's substrate selection
BIOCHEMISTRY, 45:15142-15156, DEC 26 2006
abstract, full text

Zhang, Z.Y., Boyle, P.C., Lu, B.Y., Chang, J.Y., Wriggers, W.
Entropic folding pathway of human epidermal growth factor explored by disulfide scrambling and amplified collective motion simulations
BIOCHEMISTRY, 45:15269-15278, DEC 26 2006
abstract, full text

Hemp, J., Robinson, D.E., Ganesan, K.B., Martinez, T.J., Kelleher, N.L., Gennis, R.B.
Evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases
BIOCHEMISTRY, 45:15405-15410, DEC 26 2006
abstract, full text

Cerutti, M.L., Ferreiro, D.U., Sanguineti, S., Goldbaum, F.A., de Prat-Gay, G.
Antibody recognition of a flexible epitope at the DNA binding site of the human papillomavirus transcriptional regulator E2
BIOCHEMISTRY, 45:15520-15528, DEC 26 2006
abstract, full text

Malek, K., Maghari, A.
Translocation and interactions of L-arabinose in OmpF porin: A molecular dynamics study
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 352:104-110, JAN 5 2007
abstract, full text

Milland, J., Sandrin, M.S.
ABO blood group and related antigens, natural antibodies and transplantation
TISSUE ANTIGENS, 68:459-466, DEC 2006
abstract, full text

Tarus, B., Straub, J.E., Thirumalai, D.
Dynamics of Asp23-Lys28 salt-bridge formation in A beta(10-35) monomers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:16159-16168, DEC 20 2006
abstract, full text

Rozhenko, A.B., Schoeller, W.W., Letzel, M.C., Decker, B., Agena, C., Mattay, J.
Calixarenes as hosts for ammonium cations: A quantum chemical study and mass-spectrometric investigations
CHEMISTRY-A EUROPEAN JOURNAL, 12:8995-9000, DEC 4 2006
abstract, full text

Sammalkorpi, M., Lazaridis, T.
Modeling a spin-labeled fusion peptide in a membrane: Implications for the interpretation of EPR experiments
BIOPHYSICAL JOURNAL, 92:10-22, JAN 2007
abstract, full text

Huang, A., Stultz, C.M.
Conformational sampling with implicit solvent models: Application to the PHF6 peptide in tau protein
BIOPHYSICAL JOURNAL, 92:34-45, JAN 2007
abstract, full text

Chen, H.N., Ilan, B., Wu, Y.J., Zhu, F.Q., Schulten, K., Voth, G.A.
Charge delocalization in proton channels, I: The aquaporin channels and proton blockage
BIOPHYSICAL JOURNAL, 92:46-60, JAN 2007
abstract, full text

Corradi, J., Spitzmaul, G., De Rosa, M.J., Costabel, M., Bouzat, C.
Role of pairwise interactions between M1 and M2 domains of the nicotinic receptor in channel gating
BIOPHYSICAL JOURNAL, 92:76-86, JAN 2007
abstract, full text

Doxastakis, M., Sakai, V.G., Ohtake, S., Maranas, J.K., de Pablo, J.J.
A molecular view of melting in anhydrous phospholipidic membranes
BIOPHYSICAL JOURNAL, 92:147-161, JAN 2007
abstract, full text

Dror, O., Lasker, K., Nussinov, R., Wolfson, H.
EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 63:42-49, JAN 2007
abstract, full text

Kuttel, M., Gain, J., Burger, A., Eborn, I.
Techniques for visualization of carbohydrate molecules
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 25:380-388, NOV 2006
abstract, full text

Gopal, S.M., Wenzel, W.
De novo folding of the DNA-binding ATF-2 zinc finger motif in an all-atom free-energy forcefield
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 45:7726-7728, 2006
full text

Charette, B.D., MacDonald, R.G., Wetzel, S., Berkowitz, D.B., Waldmann, H.
Protein structure similarity clustering: Dynamic treatment of PDB structures facilitates clustering
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 45:7766-7770, 2006
full text

White, S.H.
Rhomboid intramembrane protease structures galore!
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 13:1049-1051, DEC 2006
abstract, full text

Michel, J., Verdonk, M.L., Essex, J.W.
Protein-ligand binding affinity predictions by implicit solvent simulations: A tool for lead optimization?
JOURNAL OF MEDICINAL CHEMISTRY, 49:7427-7439, DEC 14 2006
abstract, full text

Lodhi, M.A., Hussain, J., Abbasi, M.A., Jassbi, A.R., Choudhary, M.I., Ahmad, V.U.
A new Bacillus pasteurii urease inhibitor from Euphorbia decipiens
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 21:531-535, OCT 2006
abstract, full text

Sadiq, S.K., Zasada, S.J., Coveney, P.V.
Grid assisted ensemble molecular dynamics simulations of HIV-1 proteases reveal novel conformations of the inhibitor saquinavir
COMPUTATIONAL LIFE SCIENCES II, PROCEEDINGS, 4216:150-161, 2006
abstract, full text

Batten, C.A., Clarke, I.N., Kempster, S.L., Oliver, S.L., Bridger, J.C., Lambden, P.R.
Characterization of a cross-reactive linear epitope in human genogroup I and bovine genogroup III norovirus capsid proteins
VIROLOGY, 356:179-187, DEC 2006
abstract, full text

Muller, M., Katsov, K., Schick, M.
Biological and synthetic membranes: What can be learned from a coarse-grained description?
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 434:113-176, NOV 2006
abstract, full text

Vargiu, A.V., Ruggerone, P., Magistrato, A., Carloni, P.
Anthramycin-DNA binding explored by molecular simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 110:24687-24695, DEC 7 2006
abstract, full text

Ballenegger, V., Picaud, S., Toubin, C.
Molecular dynamics study of diffusion of formaldehyde in ice
CHEMICAL PHYSICS LETTERS, 432:78-83, DEC 4 2006
abstract, full text

Rai, V., Gaur, M., Shukla, S., Shukla, S., Ambudkar, S.V., Komath, S.S., Prasad, R.
Conserved Asp327 of Walker B motif in the N-terminal nucleotide binding domain (NBD-1) of Cdr1p of Candida albicans has acquired a new role in ATP hydrolysis
BIOCHEMISTRY, 45:14726-14739, DEC 12 2006
abstract, full text

Yao, S.G., Liu, M.S., Masters, S.L., Zhang, J.G., Babon, J.J., Nicola, N.A., Nicholson, S.E., Norton, R.S.
Dynamics of the SPRY domain-containing SOCS box protein 2: Flexibility of key functional loops
PROTEIN SCIENCE, 15:2761-2772, DEC 2006
abstract, full text

Levy, E.D., Pereira-Leal, J.B., Chothia, C., Teichmann, S.A.
3D complex: A structural classification of protein complexes
PLOS COMPUTATIONAL BIOLOGY, 2:1395-1406, NOV 2006
abstract, full text

Bellesia, G., Fedorov, M.V., Timoshenko, E.G.
Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 373:455-476, JAN 1 2007
abstract, full text

Murcia, M., Faraldo-Gomez, J.D., Maxfield, F.R., Roux, B.
Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol
JOURNAL OF LIPID RESEARCH, 47:2614-2630, DEC 2006
abstract, full text

Papakyriakou, A., Malandrinos, G., Garoufis, A.
Interaction of Lambda- and Delta-[Ru(bpy)(2)(pbmz)](PF6)(2) with the oligonucleotide duplex d(CGCGAATTCGCG)(2)
JOURNAL OF INORGANIC BIOCHEMISTRY, 100:1842-1848, NOV 2006
abstract, full text

Lynch, D.L., Reggio, P.H.
Cannabinoid CB1 receptor recognition of endocannabinoids via the lipid bilayer: molecular dynamics simulations of CB1 transmembrane helix 6 and anandamide in a phospholipid bilayer
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 20:495-509, AUG 2006
abstract, full text

Bazeley, P.S., Prithivi, S., Struble, C.A., Povinelli, R.J., Sem, D.S.
Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46:2698-2708, NOV 27 2006
abstract, full text

Allis, D.G., Korter, T.M.
Theoretical analysis of the terahertz spectrum of the high explosive PETN
CHEMPHYSCHEM, 7:2398-2408, NOV 13 2006
abstract, full text

Nygaard, T.P., Rovira, C., Peters, G.H., Jensen, M.O.
Ammonium recruitment and ammonia transport by E-coli ammonia channel AmtB
BIOPHYSICAL JOURNAL, 91:4401-4412, DEC 2006
abstract, full text

Arkhipov, A., Freddolino, P.L., Imada, K., Namba, K., Schulten, K.
Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum
BIOPHYSICAL JOURNAL, 91:4589-4597, DEC 2006
abstract, full text

Johnson, C.K.
Calmodulin, conformational states, and calcium signaling. A single-molecule perspective
BIOCHEMISTRY, 45:14233-14246, DEC 5 2006
abstract, full text

Khalid, S., Sansom, M.S.P.
Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis
MOLECULAR MEMBRANE BIOLOGY, 23:499-508, NOV-DEC 2006
abstract, full text

Reddy, G., Yethiraj, A.
Implicit and explicit solvent models for the simulation of dilute polymer solutions
MACROMOLECULES, 39:8536-8542, NOV 28 2006
abstract, full text

Han, D., Namslauer, A., Pawate, A., Morgan, J.E., Nagy, S., Vakkasoglu, A.S., Brzezinski, P., Gennis, R.B.
Replacing Asn207 by aspartate at the neck of the D channel in the aa(3)-type cytochrome c oxidase from Rhodobacter sphaeroides results in decoupling the proton pump
BIOCHEMISTRY, 45:14064-14074, NOV 28 2006
abstract, full text

Verhaest, M., Lammens, W., Le Roy, K., De Coninck, B., De Ranter, C.J., Van Laere, A., Van den Ende, W., Rabijns, A.
X-ray diffraction structure of a cell-wall invertase from Arabidopsis thaliana
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 62:1555-1563, DEC 2006
abstract, full text

Isin, B., Rader, A.J., Dhiman, H.K., Klein-Seetharaman, J., Bahar, I.
Predisposition of the dark state of rhodopsin to functional changes in structure
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 65:970-983, DEC 1 2006
abstract, full text

Rauhamaki, V., Baumann, M., Soliymani, R., Puustinen, A., Wikstrom, M.
Identification of a histidine-tyrosine cross-link in the active site of the cbb(3)-type cytochrome c oxidase from Rhodobacter sphaeroides
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:16135-16140, OCT 31 2006
abstract, full text

Wereszczynski, J., Andricioaei, I.
On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:16200-16205, OCT 31 2006
abstract, full text

Amzallag, A., Vaillant, C., Jacob, M., Unser, M., Bednar, J., Kahn, J.D., Dubochet, J., Stasiak, A., Maddocks, J.H.
3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy
NUCLEIC ACIDS RESEARCH, 34: Art. No. e125, OCT 2006
abstract, full text

McCrate, N.E., Varner, M.E., Kim, K.I., Nagan, M.C.
Molecular dynamics simulations of human tRNA (Lys,3)(UUU) : the role of modified bases in mRNA recognition
NUCLEIC ACIDS RESEARCH, 34:5361-5368, NOV 2006
abstract, full text

Mao, J.H., Mukherjee, S., Zhang, Y., Cao, R., Sanders, J.M., Song, Y.C., Zhang, Y.H., Meints, G.A., Gao, Y.G., Mukkamala, D., Hudock, M.P., Oldfield, E.
Solid-state NMR, crystallographic, and computational investigation of Bisphosphonates and farnesyl diphosphate synthase-bisphosphonate complexes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:14485-14497, NOV 15 2006
abstract, full text

Sato, Y., Hata, M., Neya, S., Hoshino, T.
Computational analysis of the proton translocation from Asp96 to Schiff base in bacteriorhodopsin
JOURNAL OF PHYSICAL CHEMISTRY B, 110:22804-22812, NOV 16 2006
abstract, full text

Gogonea, V., Shy, J.M., Biswas, P.K.
Electronic structure, ionization potential, and electron affinity of the enzyme cofactor (6R)-5,6,7,8-tetrahydrobiopterin in the gas phase, solution, and protein environments
JOURNAL OF PHYSICAL CHEMISTRY B, 110:22861-22871, NOV 16 2006
abstract, full text

Busini, V., Moiani, D., Moscatelli, D., Zamolo, L., Cavallotti, C.
Investigation of the influence of spacer arm on the structural evolution of affinity ligands supported on agarose
JOURNAL OF PHYSICAL CHEMISTRY B, 110:23564-23577, NOV 23 2006
abstract, full text

Hubschle, C.B., Luger, P.
MolIso - a program for colour-mapped iso-surfaces
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 39:901-904, DEC 2006
abstract, full text

English, C.M., Adkins, M.W., Carson, J.J., Churchill, M.E.A., Tyler, J.K.
Structural basis for the histone chaperone activity of Asf1
CELL, 127:495-508, NOV 3 2006
abstract, full text

Cailliez, F., Lavery, R.
Dynamics and stability of E-cadherin dimers
BIOPHYSICAL JOURNAL, 91:3964-3971, DEC 2006
abstract, full text

Yin, Y., Jensen, M.O., Tajkhorshid, E., Schulten, K.
Sugar binding and protein conformational changes in lactose permease
BIOPHYSICAL JOURNAL, 91:3972-3985, DEC 2006
abstract, full text

Liu, M.S., Todd, B.D., Sadus, R.J.
Dynamic and coordinating domain motions in the active subunits of the F-1-ATPase molecular motor
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1764:1553-1560, OCT 2006
abstract, full text

Urbanc, B., Borreguero, J.M., Cruz, L., Stanley, H.E.
Ab initio discrete molecular dynamics approach to protein folding and aggregation
AMYLOID, PRIONS, AND OTHER PROTEIN AGGREGATES, PT B, 412:314-338, 2006
abstract, full text

Bialonska, A., Ciunik, Z.
Hydrophobic 'lock and key' recognition of N-4-nitrobenzoylamino acid by strychnine
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE, 62:1061-1070, DEC 2006
abstract, full text

Nakagawa, N., Peyrard, M.
Modeling protein thermodynamics and fluctuations at the mesoscale
PHYSICAL REVIEW E, 74: Art. No. 041916, OCT 2006
abstract, full text

Greeley, J., Jaramillo, T.F., Bonde, J., Chorkendorff, I.B., Norskov, J.K.
Computational high-throughput screening of electrocatalytic materials for hydrogen evolution
NATURE MATERIALS, 5:909-913, NOV 2006
abstract, full text

Benetka, W., Koranda, M., Eisenhaber, F.
Protein prenylation: An (almost) comprehensive overview on discovery history, enzymology, and significance in physiology and disease
MONATSHEFTE FUR CHEMIE, 137:1241-1281, OCT 2006
abstract, full text

Beevers, A.J., Kukol, A.
Systematic molecular dynamics searching in a lipid bilayer: Application to the glycophorin A and oncogenic ErbB-2 transmembrane domains
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 25:226-233, OCT 2006
abstract, full text

Buehler, M.J.
Mesoscale modeling of mechanics of carbon nanotubes: Self-assembly, self-folding, and fracture
JOURNAL OF MATERIALS RESEARCH, 21:2855-2869, NOV 2006
abstract, full text

Izrailev, S., Zhu, F.Q., Agrafiotis, D.K.
A distance geometry heuristic for expanding the range of geometries sampled during conformational search
JOURNAL OF COMPUTATIONAL CHEMISTRY, 27:1962-1969, DEC 2006
abstract, full text

Lee, P.A., Orriss, G.L., Buchanan, G., Greene, N.P., Bond, P.J., Punginelli, C., Jack, R.L., Sansom, M.S.P., Berks, B.C., Palmer, T.
Cysteine-scanning mutagenesis and disulfide mapping studies of the conserved domain of the twin-arginine translocase TatB component
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:34072-34085, NOV 10 2006
abstract, full text

Benz, R.W., Nanda, H., Castro-Roman, F., White, S.H., Tobias, D.J.
Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations
BIOPHYSICAL JOURNAL, 91:3617-3629, NOV 2006
abstract, full text

Freddolino, P.L., Dittrich, M., Schulten, K.
Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins
BIOPHYSICAL JOURNAL, 91:3630-3639, NOV 2006
abstract, full text

Nienhaus, K., Renzi, F., Vallone, B., Wiedenmann, J., Nienhaus, G.U.
Exploring chromophore-protein interactions in fluorescent protein cmFP512 from Cerianthus membranaceus: X-ray structure analysis and optical spectroscopy
BIOCHEMISTRY, 45:12942-12953, OCT 31 2006
abstract, full text

Haider, S., Hall, B.A., Sansom, M.S.P.
Simulations of a protein translocation pore: SecY
BIOCHEMISTRY, 45:13018-13024, OCT 31 2006
abstract, full text

Dumont, C., Matsumura, Y., Kim, S.J., Li, J.S., Kondrashkina, E., Kihara, H., Gruebele, M.
Solvent-tuning the collapse and helix formation time scales of lambda(*)(6-85)
PROTEIN SCIENCE, 15:2596-2604, NOV 2006
abstract, full text

Juraszek, J., Bolhuis, P.G.
Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:15859-15864, OCT 24 2006
abstract, full text

Wriggers, W., Zhang, Z., Shah, M., Sorensen, D.C.
Simulating nanoscale functional motions of biomolecules
MOLECULAR SIMULATION, 32:803-815, AUG-SEP 2006
abstract, full text

Gullingsrud, J., Babakhani, A., McCammon, J.A.
Computational investigation of pressure profiles in lipid bilayers with embedded proteins
MOLECULAR SIMULATION, 32:831-838, AUG-SEP 2006
abstract, full text

Al-Sabi, A., McArthur, J., Ostroumov, V., French, R.J.
Marine toxins that target voltage-gated sodium channels
MARINE DRUGS, 4:157-192, APR 2006
abstract, full text

Cruz-Chu, E.R., Aksimentiev, A., Schulten, K.
Water-silica force field for simulating nanodevices
JOURNAL OF PHYSICAL CHEMISTRY B, 110:21497-21508, NOV 2 2006
abstract, full text

Nagai, Y., Unsworth, L.D., Koutsopoulos, S., Zhang, S.G.
Slow release of molecules in self-assembling peptide nanofiber scaffold
JOURNAL OF CONTROLLED RELEASE, 115:18-25, SEP 28 2006
abstract, full text

Hoffmann, M., Eitner, K., von Grotthuss, M., Rychlewski, L., Banachowicz, E., Grabarkiewicz, T., Szkoda, T., Kolinski, A.
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 20:305-319, MAY 2006
abstract, full text

Puklin-Faucher, E., Gao, M., Schulten, K., Vogel, V.
How the headpiece hinge angle is opened: new insights into the dynamics of integrin activation
JOURNAL OF CELL BIOLOGY, 175:349-360, OCT 23 2006
abstract, full text

Neduva, V., Russell, R.B.
Peptides mediating interaction networks: new leads at last
CURRENT OPINION IN BIOTECHNOLOGY, 17:465-471, OCT 2006
abstract, full text

Grant, B.J., Rodrigues, A.P.C., ElSawy, K.M., McCammon, J.A., Caves, L.S.D.
Bio3d: an R package for the comparative analysis of protein structures
BIOINFORMATICS, 22:2695-2696, NOV 1 2006
abstract, full text

Tuukkanen, A., Verkhovsky, M.I., Laakkonen, L., Wikstrom, M.
The K-pathway revisited: A computational study on cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:1117-1121, SEP-OCT 2006
abstract, full text

Wang, P., Guliaev, A.B., Hang, B.
Metal inhibition of human N-methylpurine-DNA glycosylase activity in base excision repair
TOXICOLOGY LETTERS, 166:237-247, OCT 25 2006
abstract, full text

Segev, E., Grumbach, M., Gerber, R.B.
Evolution of conformational changes in the dynamics of small biological molecules: a hybrid MD/RRK approach
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 8:4915-4923, 2006
abstract, full text

Perry, J.L., Goldsmith, M.R., Williams, T.R., Radack, K.P., Christensen, T., Gorham, J., Pasquinelli, M.A., Toone, E.J., Beratan, D.N., Simon, J.D.
Binding of warfarin influences the acid-base equilibrium of H242 in sudlow site I of human serum albumin
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 82:1365-1369, SEP-OCT 2006
abstract, full text

Qiao, W., McLennan, M., Kennell, R., Ebert, D.S., Klimeck, G.
Hub-based simulation and graphics hardware accelerated visualization for nanotechnology applications
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 12:1061-1068, SEP-OCT 2006
abstract, full text

Yui, T., Nishimura, S., Akiba, S., Hayashi, S.
Swelling behavior of the cellulose I beta crystal models by molecular dynamics
CARBOHYDRATE RESEARCH, 341:2521-2530, NOV 6 2006
abstract, full text

Brylinski, M., Konieczny, L., Roterman, I.
Hydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor
BIOCHIMIE, 88:1229-1239, SEP 2006
abstract, full text

Balbin, A., Cardenas, C., Villaveces, J.L., Patarroyo, M.E.
A theoretical analysis of HLA-DR beta 1*0301-CLIP complex using the first three multipolar moments of the electrostatic field
BIOCHIMIE, 88:1307-1311, SEP 2006
abstract, full text

Wraight, C.A.
Chance and design - Proton transfer in water, channels and bioenergetic proteins
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:886-912, AUG 2006
abstract, full text

Mulkidjanian, A.Y., Heberle, J., Cherepanov, D.A.
Protons @ interfaces: Implications for biological energy conversion
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:913-930, AUG 2006
abstract, full text

Gutman, M., Nachliel, E., Friedman, R.
The mechanism of proton transfer between adjacent sites on the molecular surface
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:931-941, AUG 2006
abstract, full text

Moreno, M., Sani, M., Raos, G., Meille, S.V., Belotti, D., Giavazzi, R., Bellosta, S., Volonterio, A., Zanda, M.
Stereochemically pure alpha-trifluoromethyl-malic hydroxamates: synthesis and evaluation as inhibitors of matrix metalloproteinases
TETRAHEDRON, 62:10171-10181, OCT 23 2006
abstract, full text

Kampmann, T., Mueller, D.S., Mark, A.E., Young, P.R., Kobe, B.
The role of histidine residues in low-pH-mediated viral membrane fusion
STRUCTURE, 14:1481-1487, OCT 2006
abstract, full text

Falconi, M., Chillemi, G., Di Marino, D., D'Annessa, I., della Rocca, B.M., Palmieri, L., Desideri, A.
Structural dynamics of the mitochondrial ADP/ATP carrier revealed by molecular dynamics simulation studies
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 65:681-691, NOV 15 2006
abstract, full text

Blood, P.D., Voth, G.A.
Direct observation of Bin/amphiphysin/Rvs (BAR) domain-induced membrane curvature by means of molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:15068-15072, OCT 10 2006
abstract, full text

Abbate, S., Barlati, S., Colombi, M., Fornili, S.L., Francescato, P., Gangemi, F., Lebon, F., Longhi, G., Manitto, P., Recca, T., Speranza, G., Zoppi, N.
Study of conformational properties of a biologically active peptide of fibronectin by circular dichroism, NMR and molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 8:4668-4677, 2006
abstract, full text

Duff, N., Wang, J., Mann, E.K., Lacks, D.J.
Molecular dynamics investigation of bent-core molecules on a water surface
LANGMUIR, 22:9082-9085, OCT 24 2006
abstract, full text

Layten, M., Hornak, V., Simmerling, C.
The open structure of a multi-drug-resistant HIV-1 protease is stabilized by crystal packing contacts
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:13360-13361, OCT 18 2006
full text

Bussi, G., Gervasio, F.L., Laio, A., Parrinello, M.
Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:13435-13441, OCT 18 2006
abstract, full text

Herbert, J.M., Head-Gordon, M.
Charge penetration and the origin of large O-H vibrational red-shifts in hydrated-electron clusters, (H2O)(n)(-)
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:13932-13939, OCT 25 2006
abstract, full text

Diemand, A.V., Lupas, A.N.
Modeling AAA+ ring complexes from monomeric structures
JOURNAL OF STRUCTURAL BIOLOGY, 156:230-243, OCT 2006
abstract, full text

Knaup, J.M., Kohler, C., Frauenheim, T., Blumenau, A.T., Amkreutz, M., Schiffels, P., Schneider, B., Hennemann, O.D.
Computational studies on polymer adhesion at the surface of gamma-Al2O3. I. The adsorption of adhesive component molecules from the gas phase
JOURNAL OF PHYSICAL CHEMISTRY B, 110:20460-20468, OCT 19 2006
abstract, full text

Nockemann, P., Thijs, B., Pittois, S., Thoen, J., Glorieux, C., Van Hecke, K., Van Meervelt, L., Kirchner, B., Binnemans, K.
Task-specific ionic liquid for solubilizing metal oxides
JOURNAL OF PHYSICAL CHEMISTRY B, 110:20978-20992, OCT 26 2006
abstract, full text

Tepper, H.L., Voth, G.A.
Mechanisms of passive ion permeation through lipid bilayers: Insights from simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 110:21327-21337, OCT 26 2006
abstract, full text

Patel, S., Sista, P., Balaji, P.V., Sasidhar, Y.U.
beta-Hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 25:103-115, SEP 2006
abstract, full text

Yang, X.Y., Wang, M., Fitzgerald, M.C.
Direct analysis of backbone-backbone hydrogen bond formation in protein folding transition states
JOURNAL OF MOLECULAR BIOLOGY, 363:506-519, OCT 20 2006
abstract, full text

Simmons, D.P., Abregu, F.A., Krishnan, U.V., Proll, D.F., Streltsov, V.A., Doughty, L., Hattarki, M.K., Nuttall, S.D.
Dimerisation strategies for shark IgNAR single domain antibody fragments
JOURNAL OF IMMUNOLOGICAL METHODS, 315:171-184, AUG 31 2006
abstract, full text

Han, W.G., Liu, T.Q., Lovell, T., Noodleman, L.
Density functional theory study of Fe(IV) d-d optical transitions in active-site models of class I ribonucleotide reductase intermediate X with vertical self-consistent reaction field method
INORGANIC CHEMISTRY, 45:8533-8542, OCT 16 2006
abstract, full text

Poghosyan, A.H., Yeghiazaryan, G.A., Charabekyan, H.H., Shahinyan, A.A.
The GROMACS and NAMD software packages comparison
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 1:736-743, AUG 2006
abstract, full text

Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
Conformational changes of the p53-binding cleft of MDM2 revealed by molecular dynamics simulations
BIOPOLYMERS, 83:365-373, NOV 2006
abstract, full text

Foley, M.C., Arora, K., Schlick, T.
Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda
BIOPHYSICAL JOURNAL, 91:3182-3195, NOV 2006
abstract, full text

Streiff, J.H., Allen, T.W., Atanasova, E., Juranic, N., Macura, S., Penheiter, A.R., Jones, K.A.
Prediction of volatile anesthetic binding sites in proteins
BIOPHYSICAL JOURNAL, 91:3405-3414, NOV 2006
abstract, full text

Paramore, S., Voth, G.A.
Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules
BIOPHYSICAL JOURNAL, 91:3436-3445, NOV 2006
abstract, full text

Duff, N., Duong, N.H., Lacks, D.J.
Stretching the immunoglobulin 27 domain of the titin protein: The dynamic energy landscape
BIOPHYSICAL JOURNAL, 91:3446-3455, NOV 2006
abstract, full text

Ceccarelli, M., Ruggerone, P., Anedda, R., Fais, A., Era, B., Sollaino, M.C., Corda, M., Casu, M.
Structure-function relationship in a variant hemoglobin: A combined computational-experimental approach
BIOPHYSICAL JOURNAL, 91:3529-3541, NOV 2006
abstract, full text

Ruas, A., Guilbaud, P., Den Auwer, C., Moulin, C., Simonin, J.P., Turq, P., Moisy, P.
Experimental and molecular dynamics studies of dysprosium(III) salt solutions for a better representation of the microscopic features used within the binding mean spherical approximation theory
JOURNAL OF PHYSICAL CHEMISTRY A, 110:11770-11779, OCT 19 2006
abstract, full text

Jawdekar, G.W., Hanzlowsky, A., Hovde, S.L., Jelencic, B., Feig, M., Geiger, J.H., Henry, R.W.
The unorthodox SNAP50 zinc finger domain contributes to cooperative promoter recognition by human SNAP(C)
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:31050-31060, OCT 13 2006
abstract, full text

Floquet, N., Marechal, J.D., Badet-Denisot, M.A., Robert, C.H., Dauchez, M., Perahia, D.
Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors
FEBS LETTERS, 580:5130-5136, OCT 2 2006
abstract, full text

Green, D.F., Dennis, A.T., Fam, P.S., Tidor, B., Jasanoff, A.
Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide
BIOCHEMISTRY, 45:12547-12559, OCT 17 2006
abstract, full text

Virnau, P., Mirny, L.A., Kardar, M.
Intricate knots in proteins: Function and evolution
PLOS COMPUTATIONAL BIOLOGY, 2:1074-1079, SEP 2006
abstract, full text

Cheng, X.L., Wang, H.L., Grant, B., Sine, S.M., McCammon, J.A.
Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors
PLOS COMPUTATIONAL BIOLOGY, 2:1173-1184, SEP 2006
abstract, full text

de Haan, H.W., Tolokh, I.S., Gray, C.G., Goldman, S.
Nonequilibrium molecular dynamics calculation of the conductance of the KcsA potassium ion channel
PHYSICAL REVIEW E, 74: Art. No. 030905, SEP 2006
abstract, full text

Donmez, I., Patel, S.S.
Mechanisms of a ring shaped helicase
NUCLEIC ACIDS RESEARCH, 34:4216-4224, SEP 2006
abstract, full text

Papadopoulos, G., Grudinin, S., Kalpaxis, D.L., Choli-Papadopoulou, T.
Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 35:675-683, OCT 2006
abstract, full text

Roberts, E., Eargle, J., Wright, D., Luthey-Schulten, Z.
MultiSeq: unifying sequence and structure data for evolutionary analysis
BMC BIOINFORMATICS, 7: Art. No. 382, AUG 16 2006
abstract, full text

Casciari, D., Seeber, M., Fanelli, F.
Quaternary structure predictions of transmembrane proteins starting from the monomer: A docking-based approach
BMC BIOINFORMATICS, 7: Art. No. 340, JUL 12 2006
abstract, full text

Chen, X., Liu, S.Q., Sun, Z.R.
Evolutionary trace and molecular dynamics simulation of the beta2 adrenergic receptor mutation-induced activation
PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS, 33:861-868, SEP 2006
abstract, full text

Neagu, A., Kosztin, I., Jakab, K., Barz, B., Neagu, M., Jamison, R., Forgacs, G.
Computational modeling of tissue self-assembly
MODERN PHYSICS LETTERS B, 20:1217-1231, AUG 30 2006
abstract, full text

Borowski, T., Siegbahn, P.E.M.
Mechanism for catechol ring cleavage by non-heme iron intradiol dioxygenases: A hybrid DFT study
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:12941-12953, OCT 4 2006
abstract, full text

Khurana, E., Nielsen, S.O., Ensing, B., Klein, M.L.
Self-assembling cyclic peptides: Molecular dynamics studies of dimers in polar and nonpolar solvents
JOURNAL OF PHYSICAL CHEMISTRY B, 110:18965-18972, SEP 28 2006
abstract, full text

Sieffert, N., Wipff, G.
Comparing an ionic liquid to a molecular solvent in the cesium cation extraction by a calixarene: A molecular dynamics study of the aqueous interfaces
JOURNAL OF PHYSICAL CHEMISTRY B, 110:19497-19506, OCT 5 2006
abstract, full text

Meng, E.C., Pettersen, E.F., Couch, G.S., Huang, C.C., Ferrin, T.E.
Tools for integrated sequence-structure analysis with UCSF Chimera
BMC BIOINFORMATICS, 7: Art. No. 339, JUL 12 2006
abstract, full text

Fiorin, G., Pastore, A., Carloni, P., Parrinello, M.
Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail
BIOPHYSICAL JOURNAL, 91:2768-2777, OCT 2006
abstract, full text

Vemparala, S., Saiz, L., Eckenhoff, R.G., Klein, M.L.
Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles
BIOPHYSICAL JOURNAL, 91:2815-2825, OCT 2006
abstract, full text

Yesylevskyy, S.O., Kharkyanen, V.N., Demchenko, A.P.
The change of protein intradomain mobility on ligand binding: Is it a commonly observed phenomenon?
BIOPHYSICAL JOURNAL, 91:3002-3013, OCT 2006
abstract, full text

Sanbonmatsu, K.Y.
Energy landscape of the ribosomal decoding center
BIOCHIMIE, 88:1053-1059, AUG 2006
abstract, full text

Bottomley, S., Chandler, D., Morgan, E., Helmerhorst, E.
jAMVLE, A New Integrated Molecular Visualization Learning Environment
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 34:343-349, SEP-OCT 2006
abstract, full text

Bemporad, D., Sands, Z.A., Wee, C.L., Grottesi, A., Sansom, M.S.P.
Vstx1, a modifier of Kv channel gating, localizes to the interfacial region of lipid bilayers
BIOCHEMISTRY, 45:11844-11855, OCT 3 2006
abstract, full text

Dittrich, M., Schulten, K.
PcrA helicase, a prototype ATP-driven molecular motor
STRUCTURE, 14:1345-1353, SEP 2006
abstract, full text

Yu, J., Yool, A.J., Schulten, K., Tajkhorshid, E.
Mechanism of gating and ion conductivity of a possible tetrameric pore in aquaporin-1
STRUCTURE, 14:1411-1423, SEP 2006
abstract, full text

Chevrot, G., Schurhammer, R., Wipff, G.
Molecular dynamics simulations of the aqueous interface with the [BMI][PF6] ionic liquid: comparison of different solvent models
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 8:4166-4174, 2006
abstract, full text

Leontiadou, H., Mark, A.E., Marrink, S.J.
Antimicrobial peptides in action
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:12156-12161, SEP 20 2006
abstract, full text

Lee, H., Larson, R.G.
Molecular dynamics simulations of PAMAM dendrimer-induced pore formation in DPPC bilayers with a coarse-grained model
JOURNAL OF PHYSICAL CHEMISTRY B, 110:18204-18211, SEP 21 2006
abstract, full text

Petersen, M.K., Voth, G.A.
Characterization of the solvation and transport of the hydrated proton in the perfluorosulfonic acid membrane nafion
JOURNAL OF PHYSICAL CHEMISTRY B, 110:18594-18600, SEP 21 2006
full text

Jablonski, M., Kaczmarek, A., Sadlej, A.J.
Estimates of the energy of intramolecular hydrogen bonds
JOURNAL OF PHYSICAL CHEMISTRY A, 110:10890-10898, SEP 21 2006
abstract, full text

Oloo, E.O., Fung, E.Y., Tieleman, D.P.
The dynamics of the MgATP-driven closure of MalK, the energy-transducing subunit of the maltose ABC transporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:28397-28407, SEP 22 2006
abstract, full text

Rieger, R., Leung, P.S.C., Jeddeloh, M.R., Kurth, M.J., Nantz, M.H., Lam, K.S., Barsky, D., Ansari, A.A., Coppel, R.L., Mackay, I.R., Gershwin, M.E.
Identification of 2-nonynoic acid, a cosmetic component, as a potential trigger of primary biliary cirrhosis
JOURNAL OF AUTOIMMUNITY, 27:7-16, AUG 2006
abstract, full text

La Penna, G., Furlan, S., Perico, A.
Modeling H3 histone N-terminal tail and linker DNA interactions
BIOPOLYMERS, 83:135-147, OCT 5 2006
abstract, full text

Jones, P.D., Tsai, H.J., Do, Z.N., Morisseau, C., Hammock, B.D.
Synthesis and SAR of conformationally restricted inhibitors of soluble epoxide hydrolase
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 16:5212-5216, OCT 1 2006
abstract, full text

Papaleo, E., Riccardi, L., Villa, C., Fantucci, P., De Gioia, L.
Flexibility and enzymatic cold-adaptation: A comparative molecular dynamics investigation of the elastase family
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1764:1397-1406, AUG 2006
abstract, full text

Arbely, E., Granot, Z., Kass, I., Orly, J., Arkin, I.T.
A trimerizing GxxxG motif is uniquely inserted in the severe acute respiratory syndrome (SARS) coronavirus spike protein transmembrane domain
BIOCHEMISTRY, 45:11349-11356, SEP 26 2006
abstract, full text

Jun, S., Becker, J.S., Yonkunas, M., Coalson, R., Saxena, S.
Unfolding of alanine-based peptides using electron spin resonance distance measurements
BIOCHEMISTRY, 45:11666-11673, SEP 26 2006
abstract, full text

Ghosh, P., Katti, D.R., Katti, K.S.
Impact of beta-sheet conformations on the mechanical response of protein in biocomposites
MATERIALS AND MANUFACTURING PROCESSES, 21:676-682, SEP-OCT 2006
abstract, full text

Ruokoranta, T.M., Grahn, A.M., Ravantti, J.J., Poranen, M.M., Bamford, D.H.
Complete genome sequence of the broad host range single-stranded RNA phage PRR1 places it in the Levivirus genus with characteristics shared with alloleviviruses
JOURNAL OF VIROLOGY, 80:9326-9330, SEP 2006
abstract, full text

Tripet, B., Kao, D.J., Jeffers, S.A., Holmes, K.V., Hodges, R.S.
Template-based coiled-coil antigens elicit neutralizing antibodies to the SARS-coronavirus
JOURNAL OF STRUCTURAL BIOLOGY, 155:176-194, AUG 2006
abstract, full text

Sanchez, V.M., Crespo, A., Gutkind, J.S., Turjanski, A.G.
Investigation of the catalytic mechanism of farnesyl pyrophosphate synthase by computer simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 110:18052-18057, SEP 14 2006
abstract, full text

Beevers, A.J., Kukol, A.
The transmembrane domain of the oncogenic mutant ErbB-2 receptor: A structure obtained from site-specific infrared dichroism and molecular dynamics
JOURNAL OF MOLECULAR BIOLOGY, 361:945-953, SEP 1 2006
abstract, full text

Effantin, G., Boulanger, P., Neumann, E., Letellier, L., Conway, J.F.
Bacteriophage T5 structure reveals similarities with HK97 and T4 suggesting evolutionary relationships
JOURNAL OF MOLECULAR BIOLOGY, 361:993-1002, SEP 1 2006
abstract, full text

Gomaa, M.S., Yee, S.W., Milbourne, C.E., Barbera, M.C., Simons, C., Brancale, A.
Homology model of human retinoic acid metabolising enzyme cytochrome P450 26A1 (CYP26A1): Active site architecture and ligand binding
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 21:361-369, AUG 2006
abstract, full text

Ma, K., Forbes, J.G., Gutierrez-Cruz, G., Wang, K.
Titin as a giant scaffold for integrating stress and Src homology domain 3-mediated signaling pathways - The clustering of novel overlap ligand motifs in the elastic PEVK segment
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:27539-27556, SEP 15 2006
abstract, full text

Villa, A., Stock, G.
What NMR relaxation can tell us about the internal motion of an RNA hairpin: A molecular dynamics simulation study
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:1228-1236, SEP 12 2006
abstract, full text

Lamas, E.J., Balbuena, P.B.
Oxygen reduction on Pd0.75Co0.25 (111) and Pt0.75Co0.25 (111) surfaces: An ab initio comparative study
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:1388-1394, SEP 12 2006
abstract, full text

Coveney, P.V., De Fabritiis, G., Harvey, M.J., Pickles, S.M., Porter, A.R.
Coupled applications on distributed resources
COMPUTER PHYSICS COMMUNICATIONS, 175:389-396, SEP 15 2006
abstract, full text

Cavalli, A., Carloni, P., Recanatini, M.
Target-related applications of first principles quantum chemical methods in drug design
CHEMICAL REVIEWS, 106:3497-3519, SEP 13 2006
full text

Feller, C., Gunther, R., Hofmann, H.J., Grunow, M.
Molecular basis of substrate recognition in D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida
CHEMBIOCHEM, 7:1410-1418, SEP 2006
abstract, full text

Marques, A.T., Antunes, A., Fernandes, P.A., Ramos, M.J.
Comparative evolutionary genomics of the HADH2 gene encoding A beta-binding alcohol dehydrogenase/17 beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10)
BMC GENOMICS, 7: Art. No. 202, AUG 9 2006
abstract, full text

Bialonska, A., Ciunik, Z.
Isomorphous crystals of strychninium 4-chlorobenzoate and strychninium 4-nitrobenzoate
ACTA CRYSTALLOGRAPHICA SECTION C-CRYSTAL STRUCTURE COMMUNICATIONS, 62:O537-O539, SEP 2006
abstract, full text

Shehu, A., Clementi, C., Kavraki, L.E.
Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 65:164-179, OCT 1 2006
abstract, full text

Melquiond, A., Mousseau, N., Derreumaux, P.
Structures of soluble amyloid oligomers from computer simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 65:180-191, OCT 1 2006
abstract, full text

He, X.L., Dukkipati, A., Garcia, K.C.
Structural determinants of natriuretic peptide receptor specificity and degeneracy
JOURNAL OF MOLECULAR BIOLOGY, 361:698-714, AUG 25 2006
abstract, full text

Santiso, E.E., George, A.M., Gubbins, K.E., Nardelli, M.B.
Effect of confinement by porous carbons on the unimolecular decomposition of formaldehyde
JOURNAL OF CHEMICAL PHYSICS, 125: Art. No. 084711, AUG 28 2006
abstract, full text

Lamas, E.J., Albuena, P.B.
Molecular dynamics studies of a model polymer-catalyst-carbon interface
ELECTROCHIMICA ACTA, 51:5904-5911, AUG 15 2006
abstract, full text

Massi, F., Wang, C.Y., Palmer, A.G.
Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase
BIOCHEMISTRY, 45:10787-10794, SEP 12 2006
abstract, full text

Cheng, K.H., Cannon, B., Metze, J., Lewis, A., Huang, J.Y., Vaughn, M.W., Zhu, Q., Somerharju, P., Virtanen, J.
Lipid headgroup superlattice modulates the activity of surface-acting cholesterol oxidase in ternary phospholipid/cholesterol bilayers
BIOCHEMISTRY, 45:10855-10864, SEP 12 2006
abstract, full text

Song, K., Hornak, V., Santos, C.D., Grollman, A.P., Simmerling, C.
Computational analysis of the mode of binding of 8-oxoguanine to formamidopyrimidine-DNA glycosylase
BIOCHEMISTRY, 45:10886-10894, SEP 12 2006
abstract, full text

Glykos, N.M., Papanikolau, Y., Vlassi, M., Kotsifaki, D., Cesareni, G., Kokkinidis, M.
Loopless rop: Structure and dynamics of an engineered homotetrameric variant of the repressor of primer protein
BIOCHEMISTRY, 45:10905-10919, SEP 12 2006
abstract, full text

Hu, M., Chen, W., Zhang, T., Peng, Q.S.
Direct volume rendering of volumetric protein data
ADVANCES IN COMPUTER GRAPHICS, PROCEEDINGS, 4035:397-403, 2006
abstract, full text

Lim, S., Franklin, S.J.
Engineered lanthanide-binding metallohomeodomains: Designing folded chimeras by modular turn substitution
PROTEIN SCIENCE, 15:2159-2165, SEP 2006
abstract, full text

Stultz, C.M.
The folding mechanism of collagen-like model peptides explored through detailed molecular simulations
PROTEIN SCIENCE, 15:2166-2177, SEP 2006
abstract, full text

Kona, J., Brinck, T.
A combined molecular dynamics simulation and quantum chemical study on the mechanism for activation of the OxyR transcription factor by hydrogen peroxide
ORGANIC & BIOMOLECULAR CHEMISTRY, 4:3468-3478, 2006
abstract, full text

Martin, M.G., Frischknecht, A.L.
Using arbitrary trial distributions to improve intramolecular sampling in configurational-bias Monte Carlo
MOLECULAR PHYSICS, 104:2439-2456, AUG 10 2006
abstract, full text

Sikdar, D., Katti, D.R., Katti, K.S.
A molecular model for epsilon-caprolactam-based intercalated polymer clay nanocomposite: Integrating modeling and experiments
LANGMUIR, 22:7738-7747, AUG 29 2006
abstract, full text

Berrera, M., Cattaneo, A., Carloni, P.
Molecular simulation of the binding of nerve growth factor peptide mimics to the receptor tyrosine kinase A
BIOPHYSICAL JOURNAL, 91:2063-2071, SEP 2006
abstract, full text

Yu, J., Ha, T., Schulten, K.
Structure-based model of the stepping motor of PcrA helicase
BIOPHYSICAL JOURNAL, 91:2097-2114, SEP 2006
abstract, full text

Xu, J.C., Voth, G.A.
Free energy profiles for H+ conduction in the D-pathway of Cytochrome c Oxidase: A study of the wild type and N98D mutant enzymes
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:852-859, JUL 2006
abstract, full text

van der Vaart, A.
Simulation of conformational transitions
THEORETICAL CHEMISTRY ACCOUNTS, 116:183-193, AUG 2006
abstract, full text

Buehler, M.J.
Nature designs tough collagen: Explaining the nanostructure of collagen fibrils
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:12285-12290, AUG 15 2006
abstract, full text

Mitra, A., Sept, D.
Binding and interaction of dinitroanilines with apicomplexan and kinetoplastid alpha-tubulin
JOURNAL OF MEDICINAL CHEMISTRY, 49:5226-5231, AUG 24 2006
abstract, full text

McNally, D.J., Jarrell, H.C., Khieu, N.H., Li, J., Vinogradov, E., Whitfield, D.M., Szymanski, C.M., Brisson, J.R.
The HS : 19 serostrain of Campylobacter jejuni has a hyaluronic acid-type capsular polysaccharide with a nonstoichiometric sorbose branch and O-methyl phosphoramidate group
FEBS JOURNAL, 273:3975-3989, SEP 2006
abstract, full text

Ragg, E.M., Galbusera, V., Scarafoni, A., Negri, A., Tedeschi, G., Consonni, A., Sessa, F., Duranti, M.
Inhibitory properties and solution structure of a potent Bowman-Birk protease inhibitor from lentil (Lens culinaris, L) seeds
FEBS JOURNAL, 273:4024-4039, SEP 2006
abstract, full text

Bencze, K.Z., Kondapalli, K.C., Cook, J.D., McMahon, S., Millan-Pacheco, C., Pastor, N., Stemmler, T.L.
The structure and function of frataxin
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, 41:269-291, SEP-OCT 2006
abstract, full text

Brylinski, M., Konieczny, L., Roterman, I.
Hydrophobic collapse in (in silico) protein folding
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 30:255-267, AUG 2006
abstract, full text

Meyer, G.R., Gullingsrud, J., Schulten, K., Martinac, B.
Molecular dynamics study of MscL interactions with a curved lipid bilayer
BIOPHYSICAL JOURNAL, 91:1630-1637, SEP 2006
abstract, full text

Hayward, S., Kitao, A.
Molecular dynamics simulations of NAD(+)-induced domain closure in horse liver alcohol dehydrogenase
BIOPHYSICAL JOURNAL, 91:1823-1831, SEP 2006
abstract, full text

Cohen, J., Arkhipov, A., Braun, R., Schulten, K.
Imaging the migration pathways for O-2, CO, NO, and Xe inside myoglobin
BIOPHYSICAL JOURNAL, 91:1844-1857, SEP 2006
abstract, full text

Dabrowska, J., Brylinski, M.
Stereoselectivity of 8-OH-DPAT toward the serotonin 5-HT1A receptor: Biochemical and molecular modeling study
BIOCHEMICAL PHARMACOLOGY, 72:498-511, AUG 14 2006
abstract, full text

Rockwell, N.C., Su, Y.S., Lagarias, J.C.
Phytochrome structure and signaling mechanisms
ANNUAL REVIEW OF PLANT BIOLOGY, 57:837-858, 2006
abstract, full text

Esposito, L., Pedone, C., Vitagliano, L.
Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:11533-11538, AUG 1 2006
abstract, full text

Gao, M., Sotomayor, M., Villa, E., Lee, E.H., Schulten, K.
Molecular mechanisms of cellular mechanics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 8:3692-3706, 2006
abstract, full text

Guvench, O., MacKerell, A.D.
Quantum mechanical analysis of 1,2-ethanediol conformational energetics and hydrogen bonding
JOURNAL OF PHYSICAL CHEMISTRY A, 110:9934-9939, AUG 17 2006
abstract, full text

Curutchet, C., Cammi, R., Mennucci, B., Corni, S.
Self-consistent quantum mechanical model for the description of excitation energy transfers in molecules at interfaces
JOURNAL OF CHEMICAL PHYSICS, 125: Art. No. 054710, AUG 7 2006
abstract, full text

Modzelewska, A., Filipek, S., Palczewski, K., Park, P.S.H.
Arrestin interaction with rhodopsin - Conceptual models
CELL BIOCHEMISTRY AND BIOPHYSICS, 46:1-15, 2006
abstract, full text

Rebelo, S.L., Bainbridge, S.E., Amel-Kashipaz, M.R., Radford, P.M., Powell, R.J., Todd, I., Tighe, P.J.
Modeling of tumor necrosis factor receptor superfamily 1A mutants associated with tumor necrosis factor receptor-associated periodic syndrome indicates misfolding consistent with abnormal function
ARTHRITIS AND RHEUMATISM, 54:2674-2687, AUG 2006
abstract, full text

Thomas, A., Field, M.J.
A comparative QM/MM simulation study of the reaction mechanisms of human and Plasmodium falciparum HG(X) PRTases
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:10096-10102, AUG 9 2006
abstract, full text

Shi, Q., Izvekov, S., Voth, G.A.
Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel
JOURNAL OF PHYSICAL CHEMISTRY B, 110:15045-15048, AUG 10 2006
abstract, full text

Neyertz, S., Douanne, A., Brown, D.
A molecular dynamics simulation study of surface effects on gas permeation in free-standing polyimide membranes
JOURNAL OF MEMBRANE SCIENCE, 280:517-529, SEP 1 2006
abstract, full text

Buehler, M.J.
Atomistic and continuum modeling of mechanical properties of collagen: Elasticity, fracture, and self-assembly
JOURNAL OF MATERIALS RESEARCH, 21:1947-1961, AUG 2006
abstract, full text

Miyauchi, Y., Daiho, T., Yamasaki, K., Takahashi, H., Ishida-Yamamoto, A., Danko, S., Suzuki, H., Iizuka, H.
Comprehensive analysis of expression and function of 51 sarco(endo) plasmic reticulum Ca2+-ATPase mutants associated with Darier disease
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:22882-22895, AUG 11 2006
abstract, full text

Bialonska, A., Ciunik, Z.
Hydrophilic and hydrophobic pockets at surfaces of strychninium self-assemblies in pseudopolymorphous crystals of strychninium salts
CRYSTENGCOMM, 8:640-650, 2006
abstract, full text

Feniouk, B.A., Suzuki, T., Yoshida, M.
The role of subunit epsilon in the catalysis and regulation of FOF1-ATP synthase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:326-338, MAY-JUN 2006
abstract, full text

Mulkidjanian, A.Y.
Proton in the well and through the desolvation barrier
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:415-427, MAY-JUN 2006
abstract, full text

Sikdar, D., Katti, D.R., Katti, K.S., Bhowmik, R.
Insight into molecular interactions between constituents in polymer clay nanocomposites
POLYMER, 47:5196-5205, JUN 28 2006
abstract, full text

Crow, Y.J., Leitch, A., Hayward, B.E., Garner, A., Parmar, R., Griffith, E., Ali, M., Semple, C., Aicardi, J., Babul-Hirji, R., Baumann, C., Baxter, P., Bertini, E., Chandler, K.E., Chitayat, D., Cau, D., Dery, C., Fazzi, E., Goizet, C., King, M.D., Klepper, J., Lacombe, D., Lanzi, G., Lyall, H., Martinez-Frias, M.L., Mathieu, M., McKeown, C., Monier, A., Oade, Y., Quarrell, O.W., Rittey, C.D., Rogers, R.C., Sanchis, A., Stephenson, J.B.P., Tacke, U., Till, M., Tolmie, J.L., Tomlin, P., Voit, T., Weschke, B., Woods, C.G., Lebon, P., Bonthron, D.D., Ponting, C.P., Jackson, A.P.
Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutieres syndrome and mimic congenital viral brain infection
NATURE GENETICS, 38:910-916, AUG 2006
abstract, full text

Qiu, Z.J., Bossier, P., Wang, X.M., Bojikova-Fournier, S., MacRae, T.H.
Diversity, structure, and expression of the gene for p26, a small heat shock protein from Artemia
GENOMICS, 88:230-240, AUG 2006
abstract, full text

Belessi, C.J., Davi, F.B., Stamatopoulos, K.E., Degano, M., Andreou, T.M., Moreno, C., Merle-Beral, H., Crespo, M., Laoutaris, N.P., Montserrat, E., Caligaris-Cappio, F., Anagnostopoulos, A.Z., Ghia, P.
IGHV gene insertions and deletions in chronic lymphocytic leukemia: "CLL-biased" deletions in a subset of cases with stereotyped receptors
EUROPEAN JOURNAL OF IMMUNOLOGY, 36:1963-1974, JUL 2006
abstract, full text

Psachoulia, E., Bond, P.J., Sansom, M.S.P.
MD simulations of Mistic: Conformational stability in detergent micelles and water
BIOCHEMISTRY, 45:9053-9058, AUG 1 2006
abstract, full text

Velazquez-Muriel, J.A., Valle, M., Santamaria-Pang, A., Kakadiaris, I.A., Carazo, J.M.
Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies
STRUCTURE, 14:1115-1126, JUL 2006
abstract, full text

Fujiwara, S.I., Amisaki, T.
Molecular dynamics study of conformational changes in human serum albumin by binding of fatty acids
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 64:730-739, AUG 15 2006
abstract, full text

Satzger, H., Townsend, D., Zgierski, M.Z., Patchkovskii, S., Ullrich, S., Stolow, A.
Primary processes underlying the photostability of isolated DNA bases: Adenine
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:10196-10201, JUL 5 2006
abstract, full text

Pampaloni, F., Lattanzi, G., Jonas, A., Surrey, T., Frey, E., Florin, E.L.
Thermal fluctuations of grafted microtubules provide evidence of a length-dependent persistence length
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:10248-10253, JUL 5 2006
abstract, full text

Yadavalli, V.K., Forbes, J.G., Wang, K.
Functionalized self-assembled monolayers on ultraflat gold as platforms for single molecule force spectroscopy and imaging
LANGMUIR, 22:6969-6976, AUG 1 2006
abstract, full text

Qiao, R.
Control of electroosmotic flow by polymer coating: Effects of the electrical double layer
LANGMUIR, 22:7096-7100, AUG 1 2006
abstract, full text

Wu, Q., Van Voorhis, T.
Direct calculation of electron transfer parameters through constrained density functional theory
JOURNAL OF PHYSICAL CHEMISTRY A, 110:9212-9218, JUL 27 2006
abstract, full text

Hao, X.J., Varshney, A.
Geometry-guided computation of 3D electrostatics for large biomolecules
COMPUTER AIDED GEOMETRIC DESIGN, 23:545-557, AUG 2006
abstract, full text

Zhou, Q., Baumann, M.J., Piispanen, P.S., Teeri, T.T., Brumer, H.
Xyloglucan and xyloglucan endo-transglycosylases (XET): Tools for ex vivo cellulose surface modification
BIOCATALYSIS AND BIOTRANSFORMATION, 24:107-120, JAN-APR 2006
abstract, full text

Formaneck, M.S., Ma, L., Cui, Q.
Effects of temperature and salt concentration on the structural stability of human lymphotactin: Insights from molecular simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:9506-9517, JUL 26 2006
abstract, full text

Neugebauer, J., Baerends, E.J.
Exploring the ability of frozen-density embedding to model induced circular dichroism
JOURNAL OF PHYSICAL CHEMISTRY A, 110:8786-8796, JUL 20 2006
abstract, full text

Kawatsu, T., Beratan, D.N.
Electron transfer between cofactors in protein domains linked by a flexible tether
CHEMICAL PHYSICS, 326:259-269, JUL 11 2006
abstract, full text

Mulcair, M.D., Schaeffer, P.M., Oakley, A.J., Cross, H.F., Neylon, C., Hill, T.M., Dixon, N.E.
A molecular mousetrap determines polarity of termination of DNA replication in E-coli
CELL, 125:1309-1319, JUN 30 2006
abstract, full text

Reblova, K., Lankas, F., Razga, F., Krasovska, M.V., Koca, J., Sponer, J.
Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations
BIOPOLYMERS, 82:504-520, AUG 5 2006
abstract, full text

Pedersen, U.R., Leidy, C., Westh, P., Peters, G.H.
The effect of calcium on the properties of charged phospholipid bilayers
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1758:573-582, MAY 2006
abstract, full text

Iwaura, R., Shimizu, T.
Reversible photochemical conversion of helicity in self-assembled nanofibers from a 1,omega-thymidylic acid appended bolaamphiphile
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 45:4601-4604, 2006
full text

Beckstein, O., Sansom, M.S.P.
A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor
PHYSICAL BIOLOGY, 3:147-159, JUN 2006
abstract, full text

Han, B.G., Guliaev, A.B., Walian, P.J., Jap, B.K.
Water transport in AQP0 aquaporin: Molecular dynamics studies
JOURNAL OF MOLECULAR BIOLOGY, 360:285-296, JUL 7 2006
abstract, full text

Evans, D.A., Neidle, S.
Virtual screening of DNA minor groove binders
JOURNAL OF MEDICINAL CHEMISTRY, 49:4232-4238, JUL 13 2006
abstract, full text

Janosi, L., Kosztin, I., Damjanovic, A.
Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes
JOURNAL OF CHEMICAL PHYSICS, 125: Art. No. 014903, JUL 1 2006
abstract, full text

de Sancho, D., Rey, A.
Assessment of protein folding potentials with an evolutionary method
JOURNAL OF CHEMICAL PHYSICS, 125: Art. No. 014904, JUL 1 2006
abstract, full text

Henin, J., Chipot, C.
Hydrogen-bonding patterns of cholesterol in lipid membranes
CHEMICAL PHYSICS LETTERS, 425:329-335, JUL 10 2006
abstract, full text

Tsai, H.H., Gunasekaran, K., Nussinov, R.
Sequence and structure analysis of parallel beta helices: Implication for constructing amyloid structural models
STRUCTURE, 14:1059-1072, JUN 2006
abstract, full text

Sutto, L., Tiana, G., Broglia, R.A.
Sequence of events in folding mechanism: Beyond the Go model
PROTEIN SCIENCE, 15:1638-1652, JUL 2006
abstract, full text

Bond, P.J., Faraldo-Gomez, J.D., Deol, S.S., Sansom, M.S.P.
Membrane protein dynamics and detergent interactions within a crystal: A simulation study of OmpA
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:9518-9523, JUN 20 2006
abstract, full text

Pakarinen, O.H., Barth, C., Foster, A.S., Nieminen, R.M., Henry, C.R.
High-resolution scanning force microscopy of gold nanoclusters on the KBr (001) surface
PHYSICAL REVIEW B, 73: Art. No. 235428, JUN 2006
abstract, full text

Forbes, J.G., Jin, A.J., Ma, K., Gutierrez-Cruz, G., Tsai, W.L., Wang, K.A.
Titin PEVK segment: charge-driven elasticity of the open and flexible polyampholyte
JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY, 26:291-301, DEC 2005
abstract, full text

Samel, S.A., Wagner, B., Marahiel, M.A., Essen, L.O.
The thioesterase domain of the fengycin biosynthesis cluster: A structural base for the macrocyclization of a non-ribosomal lipopeptide
JOURNAL OF MOLECULAR BIOLOGY, 359:876-889, JUN 16 2006
abstract, full text

Pacios, L.F., Garcia-Arenal, F.
Comparison of properties of particles of Cucumber mosaic virus and Tomato aspermy virus based on the analysis of molecular surfaces of capsids
JOURNAL OF GENERAL VIROLOGY, 87:2073-2083, JUL 2006
abstract, full text

Leung, A.Y.T., Guo, X., He, X.Q., Jiang, H., Huang, Y.
Postbuckling of carbon nanotubes by atomic-scale finite element
JOURNAL OF APPLIED PHYSICS, 99: Art. No. 124308, JUN 15 2006
abstract, full text

Konc, J., Hodoscek, M., Janezic, D.
Molecular surface walk
CROATICA CHEMICA ACTA, 79:237-241, JUN 2006
abstract, full text

Adelroth, P., Hosler, J.
Surface proton donors for the D-pathway of cytochrome c oxidase in the absence of subunit III
BIOCHEMISTRY, 45:8308-8318, JUL 11 2006
abstract, full text

Long, K.S., Poehlsgaard, J., Kehrenberg, C., Schwarz, S., Vester, B.
The Cfr rRNA methyltransferase confers resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptograrnin A antibiotics
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 50:2500-2505, JUL 2006
abstract, full text

Zhang, Z.Y., Wriggers, W.
Local feature analysis: A statistical theory for reproducible essential dynamics of large macromolecules
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 64:391-403, AUG 1 2006
abstract, full text

Hritz, J., Zoldak, G., Sedlak, E.
Cofactor assisted Gating mechanism in the active site of NADH oxidase from Thermus thermophilus
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 64:465-476, AUG 1 2006
abstract, full text

Yoshida, T., Seko, T., Okada, O., Iwata, K., Liu, L.J., Miki, K., Yohda, M.
Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 64:502-512, AUG 1 2006
abstract, full text

Choi, E.J., Mayo, S.L.
Generation and analysis of proline mutants in protein G
PROTEIN ENGINEERING DESIGN & SELECTION, 19:285-289, JUN 2006
abstract, full text

Olofsson, M., Kalinin, S., Zdunek, J., Oliveberg, M., Johansson, L.B.A.
Tryptophan-BODIPY: A versatile donor-acceptor pair for probing generic changes of intraprotein distances
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 8:3130-3140, 2006
abstract, full text

Luo, M.X., Mazyar, O.A., Zhu, Q., Vaughn, M.W., Hase, W.L., Dai, L.L.
Molecular dynamics simulation of nanoparticle self-assembly at a liquid - Liquid interface
LANGMUIR, 22:6385-6390, JUL 4 2006
abstract, full text

Liu, Z.W., Xu, Y., Tang, P.
Steered molecular dynamics simulations of Na+ permeation across the gramicidin a channel
JOURNAL OF PHYSICAL CHEMISTRY B, 110:12789-12795, JUN 29 2006
abstract, full text

Sieffert, N., Wipff, G.
The [BMI][Tf2N] ionic liquid/water binary system: A molecular dynamics study of phase separation and of the liquid-liquid interface
JOURNAL OF PHYSICAL CHEMISTRY B, 110:13076-13085, JUL 6 2006
abstract, full text

Lee, M., Lloyd, P., Zhang, X.Y., Schallhorn, J.M., Sugimoto, K., Leach, A.G., Sapiro, G., Houk, K.N.
Shapes of antibody binding sites: Qualitative and quantitative analyses based on a geomorphic classification scheme
JOURNAL OF ORGANIC CHEMISTRY, 71:5082-5092, JUL 7 2006
abstract, full text

Hawthorne, R., Cromer, B.A., Ng, H.L., Parker, M.W., Lynch, J.W.
Molecular determinants of ginkgolide binding in the glycine receptor pore
JOURNAL OF NEUROCHEMISTRY, 98:395-407, JUL 2006
abstract, full text

Heckmann-Pohl, D.M., Bastian, S., Altmeier, S., Antes, I.
Improvement of the fungal enzyme pyranose 2-oxidase using protein engineering
JOURNAL OF BIOTECHNOLOGY, 124:26-40, JUN 25 2006
abstract, full text

Eargle, J., Luthey-Schulten, Z.
Visualizing the dual space of biological molecules
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 30:219-226, JUN 2006
abstract, full text

Czekster, R.M., de Souza, O.N.
Sim VIZ - A desktop virtual environment for visualization and analysis of protein multiple simulation trajectories
COMPUTATIONAL SCIENCE AND ITS APPLICATIONS - ICCSA 2006, PT 1, 3980:202-211, 2006
abstract, full text

Cox, D.L., Pan, J.P., Singh, R.R.P.
A mechanism for copper inhibition of infectious prion conversion
BIOPHYSICAL JOURNAL, 91:L11-L13, JUL 15 2006
abstract, full text

Fowler, P.W., Coveney, P.V.
A computational protocol for the integration of the monotopic protein prostaglandin H2 synthase into a phospholipid bilayer
BIOPHYSICAL JOURNAL, 91:401-410, JUL 15 2006
abstract, full text

Pabon, G., Amzel, L.M.
Mechanism of titin unfolding by force: Insight from quasi-equilibrium molecular dynamics calculations
BIOPHYSICAL JOURNAL, 91:467-472, JUL 15 2006
abstract, full text

Vaccaro, L., Koronakis, V., Sansom, M.S.P.
Flexibility in a drug transport accessory protein: Molecular dynamics simulations of MexA
BIOPHYSICAL JOURNAL, 91:558-564, JUL 15 2006
abstract, full text

Krasovska, M.V., Sefcikova, J., Reblova, K., Schneider, B., Walter, N.G., Sponer, J.
Cations and hydration in catalytic RNA: Molecular dynamics of the hepatitis delta virus ribozyme
BIOPHYSICAL JOURNAL, 91:626-638, JUL 15 2006
abstract, full text

Tapley, T.L., Cupp-Vickery, J.R., Vickery, L.E.
Structural determinants of HscA peptide-binding specificity
BIOCHEMISTRY, 45:8058-8066, JUL 4 2006
abstract, full text

Kocanova, S., Hornakova, T., Hritz, J., Jancura, D., Chorvat, D., Mateasik, A., Ulicny, J., Refregiers, M., Maurizot, J.C., Miskovsky, P.
Characterization of the interaction of hypericin with protein kinase c in U-87 MG human glioma cells
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 82:720-728, MAY-JUN 2006
abstract, full text

Rodziewicz, P., Rutkowski, K.S., Melikova, S.M., Koll, A., Buda, F.
Car-Parrinello molecular dynamics study of the blue-shifted F3CH center dot center dot center dot FCD3 system in liquid N-2
CHEMPHYSCHEM, 7:1221-1228, JUN 12 2006
abstract, full text

Bastug, T., Patra, S.M., Kuyucak, S.
Molecular dynamics simulations of gramicidin A in a lipid bilayer: From structure-function relations to force fields
CHEMISTRY AND PHYSICS OF LIPIDS, 141:197-204, JUN 2006
abstract, full text

Bastug, T., Kuyucak, S.
Molecular dynamics simulations of calcium binding in gramicidin A
CHEMICAL PHYSICS LETTERS, 424:82-85, JUN 12 2006
abstract, full text

Hagan, M.F., Chandler, D.
Dynamic pathways for viral capsid assembly
BIOPHYSICAL JOURNAL, 91:42-54, JUL 2006
abstract, full text

Tama, F., Brooks, C.L.
Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE, 35:115-133, 2006
abstract, full text

Takamoto, K., Chance, M.R.
Radiolytic protein footprinting with mass Spectrometry to probe the structure of macromolecular complexes
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE, 35:251-276, 2006
abstract, full text

Aranda, R., Levin, E.J., Schotte, F., Anfinrud, P.A., Phillips, G.N.
Time-dependent atomic coordinates for the dissociation of carbon monoxide from myoglobin
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 62:776-783, JUL 2006
abstract, full text

Mulkidjanian, A.Y., Cherepanov, D.A.
Probing biological interfaces by tracing proton passage across them
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 5:577-587, 2006
abstract, full text

Pelmenschikov, V., Siegbahn, P.E.M.
Nickel superoxide dismutase reaction mechanism studied by hybrid density functional methods
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:7466-7475, JUN 14 2006
abstract, full text

Nilsson, L.M., Thomas, W.E., Trintchina, E., Vogel, V., Sokurenko, E.V.
Catch bond-mediated adhesion without a shear threshold - Trimannose versus monomannose interactions with the FimH adhesin of Escherichia coli
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:16656-16663, JUN 16 2006
abstract, full text

Nieber, H., Doll, K., Zwicknagl, G.
Ab initio correlation approach to a ferric wheel-like molecular cluster
EUROPEAN PHYSICAL JOURNAL B, 51:215-221, MAY 2006
abstract, full text

Sebestik, J., Hlavacek, J., Stibor, I.
Rational design and synthesis of a double-stranded DNA-binder library
BIOPOLYMERS, 84:400-407, 2006
abstract, full text

Nichols, C.E., Johnson, C., Lockyer, M., Charles, I.G., Lamb, H.K., Hawkins, A.R., Stammers, D.K.
Structural characterization of Salmonella typhimurium YeaZ, an M22 O-sialoglycoprotein endopeptidase homolog
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 64:111-123, JUL 1 2006
abstract, full text

Ganoth, A., Nachliel, E., Friedman, R., Gutman, M.
Molecular dynamics study of a calmodulin-like protein with an IQ peptide: Spontaneous refolding of the protein around the peptide
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 64:133-146, JUL 1 2006
abstract, full text

Karain, W.I., Qaraeen, N.I., Ajarmah, B.
A stochastic model for correlated protein motions
PHYSICS LETTERS A, 354:497-500, JUN 12 2006
abstract, full text

Purohit, Y., Grosman, C.
Block of muscle nicotinic receptors by choline suggests that the activation and desensitization gates act as distinct molecular entities
JOURNAL OF GENERAL PHYSIOLOGY, 127:703-717, JUN 2006
abstract, full text

Mandelshtam, V.A., Frantsuzov, P.A.
Multiple structural transformations in Lennard-Jones clusters: Generic versus size-specific behavior
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 204511, MAY 28 2006
abstract, full text

Nishizawa, M., Nishizawa, K.
Interaction between K+ channel gate modifier hanatoxin and lipid bilayer membranes analyzed by molecular dynamics simulation
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 35:373-381, MAY 2006
abstract, full text

Catte, A., Patterson, J.C., Jones, M.K., Jerome, W.G., Bashtovyy, D., Su, Z.C., Gu, F.F., Chen, J.G., Aliste, M.P., Harvey, S.C., Li, L., Weinstein, G., Segrest, J.P.
Novel changes in discoidal high density lipoprotein morphology: A molecular dynamics study
BIOPHYSICAL JOURNAL, 90:4345-4360, JUN 2006
abstract, full text

Nichols, C.E., Sainsbury, S., Berrow, N.S., Alderton, D., Saunders, N.J., Stammers, D.K., Owens, R.J.
Structure of the P-II signal transduction protein of Neisseria meningitidis at 1.85 angstrom resolution
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 62:494-497, JUN 2006
abstract, full text

Villacanas, O., Rubio-Martinez, J.
Reducing CDK4/6-p16(INK4a) interface: Computational alanine scanning of a peptide bound to CDK6 protein
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 63:797-810, JUN 1 2006
abstract, full text

Formaneck, M.S., Ma, L., Cui, Q.
Reconciling the "old" and "new" views of protein allostery: A molecular simulation study of chemotaxis Y protein (CheY)
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 63:846-867, JUN 1 2006
abstract, full text

Bandyopadhyay, D., Huan, J., Liu, J.Z., Prins, J., Snoeyink, J., Wang, W., Tropsha, A.
Structure-based function inference using protein family-specific fingerprints
PROTEIN SCIENCE, 15:1537-1543, JUN 2006
abstract, full text

Spagnolo, L., Rivera-Calzada, A., Pearl, L.H., Llorca, O.
Three-dimensional structure of the human DNA-PKcs/Ku70/Ku80 complex assembled on DNA and its implications for DNA DSB repair
MOLECULAR CELL, 22:511-519, MAY 19 2006
abstract, full text

Yang, Z.Y., Zhao, Y.P.
QM/MM and classical molecular dynamics simulation of histidine-tagged peptide immobilization on nickel surface
MATERIALS SCIENCE AND ENGINEERING A-STRUCTURAL MATERIALS PROPERTIES MICROSTRUCTURE AND PROCESSING, 423:84-91, MAY 15 2006
abstract, full text

Warren, D.B., Chalmers, D.K., Hutchison, K., Dang, W.B., Pouton, C.W.
Molecular dynamics simulations of spontaneous bile salt aggregation
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS, 280:182-193, JUN 1 2006
abstract, full text

Bell, S.P., Curran, P.K., Choi, S., Mindell, J.A.
Site-directed fluorescence studies of a prokaryotic ClC antiporter
BIOCHEMISTRY, 45:6773-6782, JUN 6 2006
abstract, full text

Sharma, A.K., Sharma, S.K., Surolia, A., Surolia, N., Sarma, S.P.
Solution structures of conformationally equilibrium forms of holo-acyl carrier protein (PfACP) from Plasmodium falciparum provides insight into the mechanism of activation of ACPs
BIOCHEMISTRY, 45:6904-6916, JUN 6 2006
abstract, full text

Razga, F., Zacharias, M., Reblova, K., Koca, J., Sponer, J.
RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics
STRUCTURE, 14:825-835, MAY 2006
abstract, full text

Salsbury, F.R., Clodfelter, J.E., Gentry, M.B., Hollis, T., Scarpinato, K.D.
The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response
NUCLEIC ACIDS RESEARCH, 34:2173-2185, 2006
abstract, full text

Bren, U., Martinek, V., Florian, J.
Free energy simulations of uncatalyzed DNA replication fidelity: Structure and stability of T center dot G and dTTP center dot G terminal DNA mismatches flanked by a single dangling nucleotide
JOURNAL OF PHYSICAL CHEMISTRY B, 110:10557-10566, JUN 1 2006
abstract, full text

Sild, S., Maran, U., Lomaka, A., Karelson, M.
Open computing grid for molecular science and engineering
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46:953-959, MAY 2006
abstract, full text

McCullough, B.J., Eastwood, H., Clark, D.J., Polfer, N.C., Campopiano, D.J., Dorin, J.A., Maxwell, A., Langley, R.J., Govan, J.R.W., Bernstein, S.L., Bowers, M.T., Barran, P.E.
Characterisation of DEFB107 by mass spectrometry: Lessons from an anti-antimicrobial defensin
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 252:180-188, MAY 15 2006
abstract, full text

Yio, X., Diamond, M., Zhang, J.Y., Weinstein, H., Wang, L.H., Werther, L., Itzkowitz, S.
Trefoil factor family-1 mutations enhance gastric cancer cell invasion through distinct signaling pathways
GASTROENTEROLOGY, 130:1696-1706, MAY 2006
abstract, full text

Shinkarev, V.P.
Ubiquinone (coenzyme Q(10)) binding sites: Low dielectric constant of the gate prevents the escape of the semiquinone
FEBS LETTERS, 580:2534-2539, MAY 15 2006
abstract, full text

Karakasidis, T.E., Vamvakopoulos, E.
Ni3+ adsorbate dynamics on a NiO(001) surface
SURFACE SCIENCE, 600:1952-1964, MAY 1 2006
abstract, full text

Qiao, R., Georgiadis, J.G., Aluru, N.R.
Differential ion transport induced electroosmosis and internal recirculation in heterogeneous osmosis membranes
NANO LETTERS, 6:995-999, MAY 2006
abstract, full text

Matsushita, H., Yamamoto, N., Meijler, M.M., Wirsching, P., Lerner, R.A., Matsushita, M., Janda, K.D.
Chiral sensing using a blue fluorescent antibody
MOLECULAR BIOSYSTEMS, 1:303-306, OCT 2005
abstract, full text

Siggel, L., Molnar, F.
Computer modelling of a type-1 collagen fibril in water. 1. Model development and validation
JOURNAL OF THE AMERICAN LEATHER CHEMISTS ASSOCIATION, 101:179-+, MAY 2006
abstract, full text

Chevrot, G., Schurhammer, R., Wipff, G.
Surfactant behavior of "ellipsoidal" dicarbollide anions: A molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 110:9488-9498, MAY 18 2006
abstract, full text

Hakobyan, D., Nazaryan, K.
Investigation of interaction between enolase and phosphoglycerate mutase using molecular dynamics simulation
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 23:625-633, JUN 2006
abstract, full text

Hamacher, K., McCammon, J.A.
Computing the amino acid specificity of fluctuations in biomolecular systems
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:873-878, MAY 2006
abstract, full text

Lorenzi, P.L., Landowski, C.P., Brancale, A., Song, X.Q., Townsend, L.B., Drach, J.C., Amidon, G.L.
N-methylpurine DNA glycosylase and 8-oxoguanine DNA glycosylase metabolize the antiviral nucleoside 2-bromo-5,6-dichloro-1-(beta-D-ribofuranosyl) benzimidazole
DRUG METABOLISM AND DISPOSITION, 34:1070-1077, JUN 2006
abstract, full text

Adcock, S.A., McCammon, J.A.
Molecular dynamics: Survey of methods for simulating the activity of proteins
CHEMICAL REVIEWS, 106:1589-1615, MAY 2006
full text

Project, E., Friedman, R., Nachliel, E., Gutman, M.
A molecular dynamics study of the effect of Ca2+ removal on calmodulin structure
BIOPHYSICAL JOURNAL, 90:3842-3850, JUN 2006
abstract, full text

Bastug, T., Kuyucak, S.
Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations
BIOPHYSICAL JOURNAL, 90:3941-3950, JUN 2006
abstract, full text

Oard, S., Karki, B.
Mechanism of beta-purothionin antimicrobial peptide inhibition by metal ions: Molecular dynamics simulation study
BIOPHYSICAL CHEMISTRY, 121:30-43, APR 20 2006
abstract, full text

James, S., Maresca, K.P., Allis, D.G., Valliant, J.F., Eckelman, W., Babich, J.W., Zubieta, J.
Extension of the single amino acid chelate concept (SAAC) to bifunctional biotin analogues for complexation of the M(CO)(3)(+1) core (M = Tc and Re): Syntheses, characterization, biotinidase stability, and avidin binding
BIOCONJUGATE CHEMISTRY, 17:579-589, MAY 17 2006
abstract, full text

Sharma, V., Puustinen, A., Wikstrom, M., Laakkonen, L.
Sequence analysis of the cbb(3) oxidases and an atomic model for the Rhodobacter sphaeroides enzyme
BIOCHEMISTRY, 45:5754-5765, MAY 9 2006
abstract, full text

Casoli, C., Pilotti, E., Perno, C.F., Balestra, E., Polverini, E., Cassone, A., Conti, S., Magliani, W., Polonelli, L.
A killer mimotope with therapeutic activity against AIDS-related opportunistic micro-organisms inhibits ex-vivo HIV-1 replication
AIDS, 20:975-980, APR 24 2006
abstract, full text

Rai, P., Padala, C., Poon, V., Saraph, A., Basha, S., Kate, S., Tao, K., Mogridge, J., Kane, R.S.
Statistical pattern matching facilitates the design of polyvalent inhibitors of anthrax and cholera toxins
NATURE BIOTECHNOLOGY, 24:582-586, MAY 2006
abstract, full text

Nifosi, R., Tozzini, V.
Cis-trans photolsomerization of the chromophore in the green fluorescent protein variant E(2)GFP: A molecular dynamics study
CHEMICAL PHYSICS, 323:358-368, APR 21 2006
abstract, full text

Batista, P.R., Wilter, A., Durham, E.H.A.B., Pascutti, P.G.
Molecular dynamics simulations applied to the study of subtypes of HIV-1 protease common to Brazil, Africa, and Asia
CELL BIOCHEMISTRY AND BIOPHYSICS, 44:395-404, 2006
abstract, full text

Ozkirimli, E., Post, C.B.
Src kinase activation: A switched electrostatic network
PROTEIN SCIENCE, 15:1051-1062, MAY 2006
abstract, full text

Beevers, A.J., Kukol, A.
Secondary structure, orientation, and oligomerization of phospholemman, a cardiac transmembrane protein
PROTEIN SCIENCE, 15:1127-1132, MAY 2006
abstract, full text

Li, J.J., Huang, D.S., Lok, T.M., Lyu, M.R., Li, Y.X., Zhu, Y.P.
Network analysis of the protein chain tertiary structures of heterocomplexes
PROTEIN AND PEPTIDE LETTERS, 13:391-396, 2006
abstract, full text

Kezuka, Y., Ohishi, M., Itoh, Y., Watanabe, J., Mitsutomi, M., Watarabe, T., Nonaka, T.
Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037
JOURNAL OF MOLECULAR BIOLOGY, 358:472-484, APR 28 2006
abstract, full text

Hamacher, K., Hubsch, A., McCammon, J.A.
A minimal model for stabilization of biomolecules by hydrocarbon cross-linking
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 164907, APR 28 2006
abstract, full text

Badhan, R., Penny, J.
In silico modelling of the interaction of flavonoids with human P-glycoprotein nucleotide-binding domain
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 41:285-295, MAR 2006
abstract, full text

Lehmann, K., Schweimer, K., Reese, G., Randow, S., Suhr, M., Becker, W.M., Vieths, S., Rosch, P.
Structure and stability of 2S albumin-type peanut allergens: implications for the severity of peanut allergic reactions
BIOCHEMICAL JOURNAL, 395:463-472, MAY 1 2006
abstract, full text

Trapani, S., Abergel, C., Gutsche, I., Horcajada, C., Fita, I., Navaza, J.
Combining experimental data for structure determination of flexible multimeric macromolecules by molecular replacement
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 62:467-475, MAY 2006
abstract, full text

Schwieters, C.D., Kuszewski, J.J., Clore, G.M.
Using Xplor-NIH for NMR molecular structure determination
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, 48:47-62, MAR 31 2006
full text

Chaumont, A., Wipff, G.
Halide anion solvation and recognition by a macrotricyclic tetraammonium host in an ionic liquid: a molecular dynamics study
NEW JOURNAL OF CHEMISTRY, 30:537-545, APR 2006
abstract, full text

Kim, T., Rhee, A., Yip, C.M.
Force-induced insulin dimer dissociation: A molecular dynamics study
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:5330-5331, APR 26 2006
full text

Tuszynsk, J.A., Carpenter, E.J., Huzil, J.T., Malinski, W., Luchko, T., Luduena, R.F.
The evolution of the structure of tubulin and its potential consequences for the role and function of microtubules in cells and embryos
INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY, 50:341-358, 2006
abstract, full text

Hakobyan, D., Nazaryan, K.
Molecular dynamics simulation of interactions in glycolytic enzymes
BIOCHEMISTRY-MOSCOW, 71:370-375, APR 2006
abstract, full text

Polverini, E., Cugini, G., Annoni, F., Abbruzzetti, S., Viappiani, C., Gensch, T.
Molten globule formation in apomyoglobin monitored by the fluorescent probe nile red
BIOCHEMISTRY, 45:5111-5121, APR 25 2006
abstract, full text

Mukherjee, A., Bagchi, B.
Anomalous orientation-dependent effective pair interaction among histidine and other amino acid residues in metalloproteins: Breakdown of the hydropathy scale index
BIOCHEMISTRY, 45:5129-5139, APR 25 2006
abstract, full text

Strahs, D., Zhu, C.X., Cheng, B.K., Chen, J., Tse-Dinh, Y.C.
Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I
NUCLEIC ACIDS RESEARCH, 34:1785-1797, 2006
abstract, full text

Graf, E.R., Kang, Y., Hauner, A.M., Craig, A.M.
Structure function and splice site analysis of the synaptogenic activity of the neurexin-1 beta LNS domain
JOURNAL OF NEUROSCIENCE, 26:4256-4265, APR 19 2006
abstract, full text

Sotomayor, M., van der Straaten, T.A., Ravaioli, U., Schulten, K.
Electrostatic properties of the mechanosensitive channel of small conductance MscS
BIOPHYSICAL JOURNAL, 90:3496-3510, MAY 2006
abstract, full text

Spronk, S.A., Elmore, D.E., Dougherty, D.A.
Voltage-dependent hydration and conduction properties of the hydrophobic pore of the mechanosensitive channel of small conductance
BIOPHYSICAL JOURNAL, 90:3555-3569, MAY 2006
abstract, full text

Kotaka, M., Dhaliwal, B., Ren, J.S., Nichols, C.E., Angell, R., Lockyer, M., Hawkins, A.R., Stammers, D.K.
Structures of S-aureus thymidylate kinase reveal an atypical active site configuration and an intermediate conformational state upon substrate binding
PROTEIN SCIENCE, 15:774-784, APR 2006
abstract, full text

Chen, W., Chang, C.E., Gilson, M.K.
Concepts in receptor optimization: Targeting the RGD peptide
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:4675-4684, APR 12 2006
abstract, full text

Essiz, S., Coalson, R.D.
A rigid-body Newtonian propagation scheme based on instantaneous decomposition into rotation and translation blocks
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 144116, APR 14 2006
abstract, full text

Shen, L.M., Chen, Z.
A numerical study of the size and rate effects on the mechanical response of single crystal diamond and UNCD films
INTERNATIONAL JOURNAL OF DAMAGE MECHANICS, 15:169-195, APR 2006
abstract, full text

Janosi, L., Keer, H., Kosztin, I., Ritz, T.
Influence of subunit structure on the oligomerization state of light-harvesting complexes: A free energy calculation study
CHEMICAL PHYSICS, 323:117-128, MAR 31 2006
abstract, full text

Rovira, C., Alfonso-Prieto, M., Biarnes, X., Carpena, X., Fita, I., Loewen, P.C.
A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures
CHEMICAL PHYSICS, 323:129-137, MAR 31 2006
abstract, full text

Deglane, G., Abes, S., Michel, T., Prevot, P., Vives, E., Debart, F., Barvik, I., Lebleu, B., Vasseur, J.J.
Impact of the guanidinium group on hybridization and cellular uptake of cationic oligonucleotides
CHEMBIOCHEM, 7:684-692, APR 2006
abstract, full text

Lian, H.Y., Jiang, Y., Zhang, H., Jones, G.W., Perrett, S.
The yeast prion protein Ure2: Structure, function and folding
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1764:535-545, MAR 2006
abstract, full text

Kay, C.W.M., Mennenga, B., Gorisch, H., Bittl, R.
Substrate binding in quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa studied by electron-nuclear double resonance
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:5267-5272, APR 4 2006
abstract, full text

Zhang, Q.M., Marszalek, P.E.
Solvent effects on the elasticity of polysaccharide molecules in disordered and ordered states by single-molecule force spectroscopy
POLYMER, 47:2526-2532, MAR 22 2006
abstract, full text

Balaeff, A., Mahadevan, L., Schulten, K.
Modeling DNA loops using the theory of elasticity
PHYSICAL REVIEW E, 73: Art. No. 031919, MAR 2006
abstract, full text

Chipot, C., Tarek, M.
Interaction of a peptide nanotube with a water-membrane interface
PHYSICAL BIOLOGY, 3:S20-S25, MAR 2006
abstract, full text

White, S.H.
How hydrogen bonds shape membrane protein structure
PEPTIDE SOLVATION AND H-BONDS, 72:157-+, 2006
abstract, full text

Clark, M.G., Teply, J., Haarer, B.K., Viggiano, S.C., Sept, D., Amberg, D.C.
A genetic dissection of Aip1p's interactions leads to a model for Aip1p-cofilin cooperative activities
MOLECULAR BIOLOGY OF THE CELL, 17:1971-1984, APR 2006
abstract, full text

Dupuy, L.M., Rudd, R.E.
Surface identification, meshing and analysis during large molecular dynamics simulations
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, 14:229-251, MAR 2006
abstract, full text

Vrbka, L., Jungwirth, P., Bauduin, P., Touraud, D., Kunz, W.
Specific ion effects at protein surfaces: A molecular dynamics study of bovine pancreatic trypsin inhibitor and horseradish peroxidase in selected salt solutions
JOURNAL OF PHYSICAL CHEMISTRY B, 110:7036-7043, APR 6 2006
abstract, full text

Gosavi, S., Chavez, L.L., Jennings, P.A., Onuchic, J.N.
Topological frustration and the folding of interleukin-1 beta
JOURNAL OF MOLECULAR BIOLOGY, 357:986-996, MAR 31 2006
abstract, full text

Mathews, D.H., Case, D.A.
Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair
JOURNAL OF MOLECULAR BIOLOGY, 357:1683-1693, APR 14 2006
abstract, full text

Takayanagi, M., Yu, I., Nagaoka, M.
Theoretical study on the stabilities of N-terminal partial chains from apo-myoglobin
CHEMICAL PHYSICS LETTERS, 421:300-304, APR 3 2006
abstract, full text

Vasil'ev, S., Bruce, D.
A protein dynamics study of photosystem II: The effects of protein conformation on reaction center function
BIOPHYSICAL JOURNAL, 90:3062-3073, MAY 2006
abstract, full text

Gao, M., Schulten, K.
Onset of anthrax toxin pore formation
BIOPHYSICAL JOURNAL, 90:3267-3279, MAY 2006
abstract, full text

Dixit, S.B., Beveridge, D.L.
Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction
BIOINFORMATICS, 22:1007-1009, APR 15 2006
abstract, full text

Romanov, S., Wiesner, R., Myagkova, G., Kuhn, H., Ivanov, I.
Affinity Labeling of the rabbit 12/15-lipoxygenase using azido derivatives of arachidonic acid
BIOCHEMISTRY, 45:3554-3562, MAR 21 2006
abstract, full text

Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
Transient stability of the helical pattern of region F19-L22 of the N-terminal domain of p53: A molecular dynamics simulation study
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 343:110-116, APR 28 2006
abstract, full text

Corda, D., Colanzi, A., Luini, A.
The multiple activities of CtBP/BARS proteins: the Golgi view
TRENDS IN CELL BIOLOGY, 16:167-173, MAR 2006
abstract, full text

Fetrow, J.S., Knutson, S.T., Edgell, M.H.
Mutations in alpha-helical solvent-exposed sites of eglin c have long-range effects: Evidence from molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 63:356-372, MAY 1 2006
abstract, full text

Stan, G., Brooks, B.R., Lorimer, G.H., Thirumalai, D.
Residues in substrate proteins that interact witn GroEL in tne capture process are buried in the native state
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:4433-4438, MAR 21 2006
abstract, full text

Spijker, P., Vaidehi, N., Freddolino, P.L., Hilbers, P.A.J., Goddard, W.A.
Dynamic behavior of fully solvated beta 2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:4882-4887, MAR 28 2006
abstract, full text

Abild-Pedersen, F., Norskov, J.K., Rostrup-Nielsen, J.R., Sehested, J., Helveg, S.
Mechanisms for catalytic carbon nanofiber growth studied by ab initio density functional theory calculations
PHYSICAL REVIEW B, 73: Art. No. 115419, MAR 2006
abstract, full text

Mokdad, A., Krasovska, M.V., Sponer, J., Leontis, N.B.
Structural and evolutionary classification of G/U wobble basepairs in the ribosome
NUCLEIC ACIDS RESEARCH, 34:1326-1341, 2006
abstract, full text

Belevich, I., Verkhovsky, M.I., Wikstrom, M.
Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase
NATURE, 440:829-832, APR 6 2006
abstract, full text

Yu, Y.M., Chipot, C., Cai, W.S., Shao, X.G.
Molecular dynamics study of the inclusion of cholesterol into cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 110:6372-6378, MAR 30 2006
abstract, full text

Kasper, C., Pickering, D.S., Mirza, O., Olsen, L., Kristensen, A.S., Greenwood, J.R., Liljefors, T., Schousboe, A., Watjen, F., Gajhede, M., Sigurskjold, B.W., Kastrup, J.S.
The structure of a mixed GluR2 ligand-binding core dimer in complex with (S)-glutamate and the antagonist (S)-NS1209
JOURNAL OF MOLECULAR BIOLOGY, 357:1184-1201, APR 7 2006
abstract, full text

Piening, N., Nonno, R., Di Bari, M., Walter, S., Windl, O., Agrimi, U., Kretzschmar, H.A., Bertsch, U.
Conversion efficiency of bank vole prion protein in vitro is determined by residues 155 and 170, but does not correlate with the high susceptibility of bank voles to sheep scrapie in vivo
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:9373-9384, APR 7 2006
abstract, full text

Beuning, P.J., Simon, S.M., Zemla, A., Barsky, D., Walker, G.C.
A non-cleavable UmuD variant that acts as a UmuD ' mimic
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:9633-9640, APR 7 2006
abstract, full text

Noy, D., Moser, C.C., Dutton, P.L.
Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:90-105, FEB 2006
abstract, full text

Freddolino, P.L., Arkhipov, A.S., Larson, S.B., McPherson, A., Schulten, K.
Molecular dynamics simulations of the complete satellite tobacco mosaic virus
STRUCTURE, 14:437-449, MAR 2006
abstract, full text

Lee, E.H., Gao, M., Pinotsis, N., Wilmanns, M., Schulten, K.
Mechanical strength of the titin Z1Z2-telethonin complex
STRUCTURE, 14:497-509, MAR 2006
abstract, full text

Mattice, W.L., Waheed, N.
An assessment of the role of quenched randomness in the stereochemical sequences of atactic vinyl polymers
MACROMOLECULES, 39:2380-2387, MAR 21 2006
abstract, full text

Loeffler, H.H., Inada, Y., Funahashi, S.
Water exchange dynamics of lithium(I) ion in aqueous solution
JOURNAL OF PHYSICAL CHEMISTRY B, 110:5690-5696, MAR 23 2006
abstract, full text

Kawatsu, T., Beratan, D.N., Kakitani, T.
Conformationally averaged score functions for electronic propagation in proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 110:5747-5757, MAR 23 2006
abstract, full text

Ramirez, E., Santana, A., Cruz, A., Plasencia, I., Lopez, G.E.
Molecular dynamics of surfactant protein C: From single molecule to heptameric aggregates
BIOPHYSICAL JOURNAL, 90:2698-2705, APR 2006
abstract, full text

Sacquin-Mora, S., Lavery, R.
Investigating the local flexibility of functional residues in hemoproteins
BIOPHYSICAL JOURNAL, 90:2706-2717, APR 2006
abstract, full text

Pan, X.L., Tan, N.H., Zeng, G.Z., Han, H.J., Huang, H.Q.
3D-QSAR and docking studies of aldehyde inhibitors of human cathepsin K
BIOORGANIC & MEDICINAL CHEMISTRY, 14:2771-2778, APR 15 2006
abstract, full text

Khalid, S., Bond, P.J., Deol, S.S., Sansom, M.S.P.
Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 63:6-15, APR 1 2006
abstract, full text

Allis, D.G., Hudson, B.S.
Inelastic neutron scattering spectrum of Cs-2[B12H12]: Reproduction of its solid-state vibrational spectrum by periodic DFT
JOURNAL OF PHYSICAL CHEMISTRY A, 110:3744-3749, MAR 16 2006
abstract, full text

Deng, J.X., Sanchez, T., Neamati, N., Briggs, J.M.
Dynamic pharmacophore model optimization: Identification of novel HIV-1 integrase inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 49:1684-1692, MAR 9 2006
abstract, full text

Fields, P.A., Rudomin, E.L., Somero, G.N.
Temperature sensitivities of cytosolic malate dehydrogenases from native and invasive species of marine mussels (genus Mytilus): sequence-function linkages and correlations with biogeographic distribution
JOURNAL OF EXPERIMENTAL BIOLOGY, 209:656-667, FEB 2006
abstract, full text

Oliver, S.L., Batten, C.A., Deng, Y., Elschner, M., Otto, P., Charpilienne, A., Clarke, I.N., Bridger, J.C., Lambden, P.R.
Genotype 1 and genotype 2 bovine noroviruses are antigenically distinct but share a cross-reactive epitope with human noroviruses
JOURNAL OF CLINICAL MICROBIOLOGY, 44:992-998, MAR 2006
abstract, full text

Benros, C., de Brevern, A.G., Etchebest, C., Hazout, S.
Assessing a novel approach for predicting local 3D protein structures from sequence
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 62:865-880, MAR 1 2006
abstract, full text

Chen, C.Y., Beck, B.W., Krause, K., Pettitt, B.M.
Solvent participation in Serratia marcescens endonuclease complexes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 62:982-995, MAR 1 2006
abstract, full text

Favia, A.D., Cavalli, A., Masetti, M., Carotti, A., Recanatini, M.
Three-dimensional model of the human aromatase enzyme and density functional parameterization of the iron-containing protoporphyrin IX for a molecular dynamics study of heme-cysteinato cytochromes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 62:1074-1087, MAR 1 2006
abstract, full text

El-Shafey, A., Tolic, N., Young, M.M., Sale, K., Smith, R.D., Kery, V.
"Zero-length" cross-linking in solid state as an approach for analysis of protein-protein interactions
PROTEIN SCIENCE, 15:429-440, MAR 2006
abstract, full text

Polverini, E., Fornabaio, M., Fasano, A., Carlone, G., Riccio, P., Cavatorta, P.
The pH-dependent unfolding mechanism of P2 myelin protein: An experimental and computational study
JOURNAL OF STRUCTURAL BIOLOGY, 153:253-263, MAR 2006
abstract, full text

Mantz, Y.A., Chen, B., Martyna, G.J.
Structural correlations and motifs in liquid water at selected temperatures: Ab initio and empirical model predictions
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3540-3554, MAR 2 2006
abstract, full text

Baer, M., Schreiner, E., Kohlmeyer, A., Rousseau, R., Marx, D.
Inverse temperature transition of a biomimetic elastin model: Reactive flux analysis of folding/unfolding and its coupling to solvent dielectric relaxation
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3576-3587, MAR 2 2006
abstract, full text

VandeVondele, J., Lynden-Bell, R., Meijer, E.J., Sprik, M.
Density functional theory study of tetrathiafulvalene and thianthrene in acetonitrile: Structure, dynamics, and redox properties
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3614-3623, MAR 2 2006
abstract, full text

Shih, A.Y., Arkhipov, A., Freddolino, P.L., Schulten, K.
Coarse grained protein-lipid model with application to lipoprotein particles
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3674-3684, MAR 2 2006
abstract, full text

Hua, L., Huang, X.H., Zhou, R.H., Berne, B.J.
Dynamics of water confined in the interdomain region of a multidomain protein
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3704-3711, MAR 2 2006
abstract, full text

Morrone, J.A., Hasllinger, K.E., Tuckerman, M.E.
Ab initio molecular dynamics simulation of the structure and proton transport dynamics of methanol-water solutions
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3712-3720, MAR 2 2006
abstract, full text

Lee, H., Baker, J.R., Larson, R.G.
Molecular dynamics studies of the size, shape, and internal structure of 0% and 90% acetylated fifth-generation polyamidoamine dendrimers in water and methanol
JOURNAL OF PHYSICAL CHEMISTRY B, 110:4014-4019, MAR 9 2006
abstract, full text

Sieffert, N., Wipff, G.
Adsorption at the liquid-liquid interface in the biphasic rhodium catalyzed hydroformylation of olefins promoted by cyclodextrins: A molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 110:4125-4134, MAR 9 2006
abstract, full text

Konarev, P.V., Petoukhov, M.V., Volkov, V.V., Svergun, D.I.
ATSAS 2.1, a program package for small-angle scattering data analysis
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 39:277-286, APR 2006
abstract, full text

Jensen, M.O., Mouritsen, O.G.
Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF
BIOPHYSICAL JOURNAL, 90:2270-2284, APR 2006
abstract, full text

Kandasamy, S.K., Larson, R.G.
Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: A systematic investigation of hydrophobic mismatch
BIOPHYSICAL JOURNAL, 90:2326-2343, APR 2006
abstract, full text

Gumbart, J., Schulten, K.
Molecular dynamics studies of the archaeal translocon
BIOPHYSICAL JOURNAL, 90:2356-2367, APR 2006
abstract, full text

Anishkin, A., Sukharev, S., Colombini, M.
Searching for the molecular arrangement of transmembrane ceramide channels
BIOPHYSICAL JOURNAL, 90:2414-2426, APR 2006
abstract, full text

Park, J., Kahng, B., Kamm, R.D., Hwang, W.
Atomistic simulation approach to a continuum description of self-assembled beta-sheet filaments
BIOPHYSICAL JOURNAL, 90:2510-2524, APR 2006
abstract, full text

Sheng, Y.B., Wang, W.
Comparative all-atomic study of unfolding pathways for proteins chymotrypsin inhibitor 2 and barnase
PHYSICAL REVIEW E, 73: Art. No. 021915, FEB 2006
abstract, full text

Herfindal, L., Selheim, F.
Microcystin produces disparate effects on liver cells in a dose dependent manner
MINI-REVIEWS IN MEDICINAL CHEMISTRY, 6:279-285, MAR 2006
abstract, full text

Stoica, I.
Characterization of protein matrix motions in the Rb. sphaeroides photosynthetic reaction center
JOURNAL OF MOLECULAR MODELING, 12:468-480, AUG 2006
abstract, full text

Elhaji, Y.A., Stoica, I., Dennis, S., Purisima, E.O., Trifiro, M.A.
Impaired helix 12 dynamics due to proline 892 substitutions in the androgen receptor are associated with complete androgen insensitivity
HUMAN MOLECULAR GENETICS, 15:921-931, MAR 15 2006
abstract, full text

Johnston, J.M., Cook, G.A., Tomich, J.M., Sansom, M.S.P.
Conformation and environment of channel-forming peptides: A simulation study
BIOPHYSICAL JOURNAL, 90:1855-1864, MAR 2006
abstract, full text

Spaar, A., Dammer, C., Gabdoulline, R.R., Wade, R.C., Helms, V.
Diffusional encounter of barnase and barstar
BIOPHYSICAL JOURNAL, 90:1913-1924, MAR 2006
abstract, full text

Olkhova, E., Hunte, C., Screpanti, E., Padan, E., Michel, H.
Multiconformation continuum electrostatics analysis of the NhaA Na+/H+ antiporter of Escherichia coli with functional implications
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:2629-2634, FEB 21 2006
abstract, full text

Hajjar, E., Korkmaz, B., Gauthier, F., Brandsdal, B.O., Witko-Sarsat, V., Reuter, N.
Inspection of the binding sites of proteinase3 for the design of a highly specific substrate
JOURNAL OF MEDICINAL CHEMISTRY, 49:1248-1260, FEB 23 2006
abstract, full text

Moll, A., Hildebrandt, A., Lenhof, H.P., Kohlbacher, O.
BALLView: An object-oriented molecular visualization and modeling framework
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 19:791-800, NOV 2005
abstract, full text

Klix, A., Suzuki, A., Terai, T.
Study of tritium migration in liquid Li2BeF4 with ab initio molecular dynamics
FUSION ENGINEERING AND DESIGN, 81:713-717, FEB 2006
abstract, full text

Bilder, P., Lightle, S., Bainbridge, G., Ohren, J., Finzel, B., Sun, F., Holley, S., Al-Kassim, L., Spessard, C., Melnick, M., Newcomer, M., Waldrop, G.L.
The structure of the carboxyltransferase component of acetyl-CoA carboxylase reveals a zinc-binding motif unique to the bacterial enzyme
BIOCHEMISTRY, 45:1712-1722, FEB 14 2006
abstract, full text

Martinez, T.J.
Insights for light-driven molecular devices from ab initio multiple spawning excited-state dynamics of organic and biological chromophores
ACCOUNTS OF CHEMICAL RESEARCH, 39:119-126, FEB 2006
abstract, full text

Dahlberg, M., Laaksonen, A.
Preferential solvation of phenol in binary solvent mixtures. A molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY A, 110:2253-2258, FEB 16 2006
abstract, full text

Gairi, M., Saiz, P., Madurga, S., Roig, X., Erchegyi, J., Koerber, S.C., Rubi, J.C., Rivier, J.E., Giralt, E.
Conformational analysis of a potent SSTR3-selective somatostatin analogue by NMR in water solution
JOURNAL OF PEPTIDE SCIENCE, 12:82-91, FEB 2006
abstract, full text

Bialonska, A., Ciunik, Z.
When in the presence of the strong hydrogen bonds, the weak hydrogen bonds gain an importance
CRYSTENGCOMM, 8:66-74, 2006
abstract, full text

Priyakumar, U.D., MacKerell, A.D.
Computational approaches for investigating base flipping in oligonucleotides
CHEMICAL REVIEWS, 106:489-505, FEB 2006
full text

Noy, D., Dutton, P.L.
Design of a minimal polypeptide unit for bacteriochlorophyll binding and self-assembly based on photosynthetic bacterial light-harvesting proteins
BIOCHEMISTRY, 45:2103-2113, FEB 21 2006
abstract, full text

Sapay, N., Montserret, R., Chipot, C., Brass, V., Moradpour, D., Deleage, G., Penin, F.
NMR structure and molecular dynamics of the in-plane membrane anchor of nonstructural. protein 5A from bovine viral diarrhea virus
BIOCHEMISTRY, 45:2221-2233, FEB 21 2006
abstract, full text

Kneller, G.R., Calligari, P.
Efficient characterization of protein secondary structure in terms of screw motions
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 62:302-311, MAR 2006
abstract, full text

Vicens, Q., Cech, T.R.
Atomic level architecture of group I introns revealed
TRENDS IN BIOCHEMICAL SCIENCES, 31:41-51, JAN 2006
abstract, full text

Braun, O.M., Naumovets, A.G.
Nanotribology: Microscopic mechanisms of friction
SURFACE SCIENCE REPORTS, 60:79-158, FEB 2006
abstract, full text

Chaumont, A., Wipff, G.
Solvation of uranyl-CMPO complexes in dry vs. humid forms of the [BMI][PF6] ionic liquid. A molecular dynamics study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 8:494-502, JAN 28 2006
abstract, full text

Spackova, N., Sponer, J.
Molecular dynamics simulations of sarcin-ricin rRNA motif
NUCLEIC ACIDS RESEARCH, 34:697-708, 2006
abstract, full text

Liu, Y.M., Hu, X.H.
Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB - A quantum chemical analysis
JOURNAL OF PHYSICAL CHEMISTRY A, 110:1375-1381, FEB 2 2006
abstract, full text

Allis, D.G., Prokhorova, D.A., Korter, T.M.
Solid-state modeling of the terahertz spectrum of the high explosive HMX
JOURNAL OF PHYSICAL CHEMISTRY A, 110:1951-1959, FEB 9 2006
abstract, full text

Kosztin, I., Barz, B., Janosi, L.
Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 064106, FEB 14 2006
abstract, full text

Milne, J.L.S., Wu, X.W., Borgnia, M.J., Lengyel, J.S., Brooks, B.R., Shi, D., Perham, R.N., Subramaniam, S.
Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:4364-4370, FEB 17 2006
abstract, full text

van der Straaten, T.A., Kathawala, G., Ravaioli, U.
Device engineering approaches to the simulation of charge transport in biological ion channels
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 3:42-62, FEB 2006
abstract, full text

Sun, Y., Bojikova-Fournier, S., MacRae, T.H.
Structural and functional roles for beta-strand 7 in the alpha-crystallin domain of p26, a polydisperse small heat shock protein from Artemia franciscana
FEBS JOURNAL, 273:1020-1034, MAR 2006
abstract, full text

Arauzo-Bravo, M.J., Ahmad, S.
Protein sequence and structure databases: A review
CURRENT ANALYTICAL CHEMISTRY, 1:355-371, NOV 2005
abstract, full text

Radic, Z., Manetsch, R., Krasinski, A., Raushel, J., Yamauchi, J., Garcia, C., Kolb, H., Sharpless, K.B., Taylor, P.
Molecular basis of interactions of cholinesterases with tight binding inhibitors
CHEMICO-BIOLOGICAL INTERACTIONS, 157:133-141, DEC 15 2005
abstract, full text

Friedman, R., Nachliel, E., Gutman, M.
Fatty acid binding proteins: Same structure but different binding mechanisms? Molecular dynamics simulations of intestinal fatty acid binding protein
BIOPHYSICAL JOURNAL, 90:1535-1545, MAR 2006
abstract, full text

Chu, J.W., Voth, G.A.
Coarse-grained modeling of the actin filament derived from atomistic-scale simulations
BIOPHYSICAL JOURNAL, 90:1572-1582, MAR 2006
abstract, full text

Petrone, P., Pande, V.S.
Can conformational change be described by only a few normal modes?
BIOPHYSICAL JOURNAL, 90:1583-1593, MAR 2006
abstract, full text

Sands, Z.A., Grottesi, A., Sansom, M.S.P.
The intrinsic flexibility of the Kv voltage sensor and its implications for channel gating
BIOPHYSICAL JOURNAL, 90:1598-1606, MAR 2006
abstract, full text

Danelon, C., Nestorovich, E.M., Winterhalter, M., Ceccarelli, M., Bezrukov, S.M.
Interaction of zwitterionic penicillins with the OmpF channel facilitates their translocation
BIOPHYSICAL JOURNAL, 90:1617-1627, MAR 2006
abstract, full text

Richardson, C.M., Williamson, D.S., Parratt, M.J., Borgognoni, J., Cansfield, A.D., Dokurno, P., Francis, G.L., Howes, R., Moore, J.D., Murray, J.B., Robertson, A., Surgenor, A.E., Torrance, C.J.
Triazolo[1,5-a]pyrimidines as novel CDK2 inhibitors: Protein structure-guided design and SAR
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 16:1353-1357, MAR 1 2006
abstract, full text

Moll, A., Hildebrandt, A., Lenhof, H.P., Kohlbacher, O.
BALLView: a tool for research and education in molecular modeling
BIOINFORMATICS, 22:365-366, FEB 1 2006
abstract, full text

Eargle, J., Wright, D., Luthey-Schulten, Z.
Multiple Alignment of protein structures and sequences for VMD
BIOINFORMATICS, 22:504-506, FEB 15 2006
abstract, full text

Flock, U., Reimann, J., Adelroth, P.
Proton transfer in bacterial nitric oxide reductase
BIOCHEMICAL SOCIETY TRANSACTIONS, 34:188-190, FEB 2006
abstract, full text

Colacino, S., Tiana, G., Broglia, R.A., Colombo, G.
The determinants of stability in the human prion protein: Insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 62:698-707, FEB 15 2006
abstract, full text

Tan, M.L., Kang, C.H., Ichiye, T.
The role of backbone stability near Ala(44) in the high reduction potential class of rubredoxins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 62:708-714, FEB 15 2006
abstract, full text

Dima, R.I., Thirumalai, D.
Determination of network of residues that regulate allostery in protein families using sequence analysis
PROTEIN SCIENCE, 15:258-268, FEB 2006
abstract, full text

Tornroth-Horsefield, S., Wang, Y., Hedfalk, K., Johanson, U., Karlsson, M., Tajkhorshid, E., Neutze, R., Kjellbom, P.
Structural mechanism of plant aquaporin gating
NATURE, 439:688-694, FEB 9 2006
abstract, full text

Sahoo, N., Beatty, W., Heuser, J., Sept, D., Sibley, L.D.
Unusual kinetic and structural properties control rapid assembly and turnover of actin in the parasite Toxoplasma gondii
MOLECULAR BIOLOGY OF THE CELL, 17:895-906, FEB 2006
abstract, full text

Sieffert, N., Wipff, G.
Alkali cation extraction by calix[4]crown-6 to room-temperature ionic liquids. The effect of solvent anion and humidity investigated by molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 110:1106-1117, JAN 26 2006
abstract, full text

Riposati, A., Prieto, T., Shida, C.S., Nantes, I.L., Nascimento, O.R.
Low spin states of microperoxidases produced by inter- and intra-peptide chain sixth ligands: Effect of pH and the oligopeptide type
JOURNAL OF INORGANIC BIOCHEMISTRY, 100:226-238, FEB 2006
abstract, full text

Wang, T., Wade, R.C.
Force field effects on a beta-sheet protein domain structure in thermal unfolding simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:140-148, JAN-FEB 2006
abstract, full text

Huang, N., Kalyanaraman, C., Irwin, J.J., Jacobson, M.P.
Physics-based scoring of protein-ligand complexes: Enrichment of known inhibitors in large-scale virtual screening
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46:243-253, JAN-FEB 2006
abstract, full text

Warren, C.L., Kratochvil, N.C.S., Hauschild, K.E., Foister, S., Brezinski, M.L., Dervan, P.B., Phillips, G.N., Ansari, A.Z.
Defining the sequence-recognition profile of DNA-binding molecules
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:867-872, JAN 24 2006
abstract, full text

Wells, S., Menor, S., Hespenheide, B., Thorpe, M.F.
Constrained geometric simulation of diffusive motion in proteins
PHYSICAL BIOLOGY, 2:S127-S136, DEC 2005
abstract, full text

Hermann, J.C., Ridder, L., Hotje, H.D., Mulholland, A.J.
Molecular mechanisms of antibiotic resistance: QM/MM modelling of deacylation in a class A beta-lactamase
ORGANIC & BIOMOLECULAR CHEMISTRY, 4:206-210, JAN 21 2006
abstract, full text

Hetenyi, C., Paragi, G., Maran, U., Timar, Z., Karelson, M., Penke, B.
Combination of a modified scoring function with two-dimensional descriptors for calculation of binding affinities of bulky, flexible ligands to proteins
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:1233-1239, FEB 1 2006
abstract, full text

Arluison, W., Mura, C., Guzman, M.R., Liquier, J., Pellegrini, O., Gingery, M., Regnier, P., Marco, S.
Three-dimensional structures of fibrillar Sm proteins: Hfq and other Sm-like proteins
JOURNAL OF MOLECULAR BIOLOGY, 356:86-96, FEB 10 2006
abstract, full text

Moore, M.J.B., Schultes, C.M., Cuesta, J., Cuenca, F., Gunaratnam, M., Tanious, F.A., Wilson, W.D., Neidle, S.
Trisubstituted acridines as G-quadruplex telomere targeting agents. Effects of extensions of the 3,6-and 9-side chains on quadruplex binding, telomerase activity, and cell proliferation
JOURNAL OF MEDICINAL CHEMISTRY, 49:582-599, JAN 26 2006
abstract, full text

Patargias, G., Zitzmann, N., Dwek, R., Fischer, W.B.
Protein-protein interactions: Modeling the hepatitis C virus ion channel p7
JOURNAL OF MEDICINAL CHEMISTRY, 49:648-655, JAN 26 2006
abstract, full text

Bronson, J., Lee, O.S., Saven, J.G.
Molecular dynamics simulation of WSK-3, a computationally designed, water-soluble variant of the integral membrane protein KcsA
BIOPHYSICAL JOURNAL, 90:1156-1163, FEB 2006
abstract, full text

Henin, J., Maigret, B., Tarek, M., Escrieut, C., Fourmy, D., Chipot, C.
Probing a model of a GPCR/ligand complex in an explicit membrane environment: The human cholecystokinin-1 receptor
BIOPHYSICAL JOURNAL, 90:1232-1240, FEB 2006
abstract, full text

Bayas, M.V., Leung, A., Evans, E., Leckband, D.
Lifetime measurements reveal kinetic differences between homophilic cadherin bonds
BIOPHYSICAL JOURNAL, 90:1385-1395, FEB 2006
abstract, full text

Legge, F.S., Budi, A., Treutlein, H., Yarovsky, I.
Protein flexibility: Multiple molecular dynamics simulations of insulin chain B
BIOPHYSICAL CHEMISTRY, 119:146-157, JAN 20 2006
abstract, full text

Li, C., Gershon, P.D.
pK(a) of the mRNA cap-specific 2 '-O-methyltransferase catalytic lysine by HSQC NMR detection of a two-carbon probe
BIOCHEMISTRY, 45:907-917, JAN 24 2006
abstract, full text

Gullingsrud, J., Kim, C., Taylor, S.S., McCammon, J.A.
Dynamic binding of PKA regulatory subunit RI alpha
STRUCTURE, 14:141-149, JAN 2006
abstract, full text

Zhang, D.Q., McCammon, J.A.
The association of tetrameric acetylcholinesterase with CoIQ tail: A block normal mode analysis
PLOS COMPUTATIONAL BIOLOGY, 1:484-491, NOV 2005
abstract, full text

Law, M.J., Linde, M.E., Chambers, E.J., Oubridge, C., Katsamba, P.S., Nilsson, L., Haworth, I.S., Laird-Offringa, I.A.
The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA
NUCLEIC ACIDS RESEARCH, 34:275-285, 2006
abstract, full text

Barder, T.E.
Synthesis, structural, and electron topographical analyses of a dialkylbiaryl phosphine/arene-ligated palladium(I) dimer: Enhanced reactivity in Suzuki-Miyaura coupling reactions
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:898-904, JAN 25 2006
abstract, full text

Biarnes, X., Nieto, J., Planas, A., Rovira, C.
Substrate distortion in the michaelis complex of Bacillus 1,3-1,4-beta-glucanase - Insight from first principles molecular dynamics simulations
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:1432-1441, JAN 20 2006
abstract, full text

Correia, B.E., Loureiro-Ferreira, N., Rodrigues, J.R., Brito, R.M.M.
A structural model of an amyloid protofilament of transthyretin
PROTEIN SCIENCE, 15:28-32, JAN 2006
abstract, full text

Wang, Y.L., Arora, K., Schlick, T.
Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass
PROTEIN SCIENCE, 15:135-151, JAN 2006
abstract, full text

Park, S., Saven, J.G.
Simulation of pH-dependent edge strand rearrangement in human beta-2 microglobulin
PROTEIN SCIENCE, 15:200-207, JAN 2006
abstract, full text

Lee, I.R., Lee, W., Zewail, A.H.
Primary steps of the photoactive yellow protein: Isolated chromophore dynamics and protein directed function
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:258-262, JAN 10 2006
abstract, full text

Branden, G., Pawate, A.S., Gennis, R.B., Brzezinski, P.
Controlled uncoupling and recoupling of proton pumping in cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:317-322, JAN 10 2006
abstract, full text

Tanizaki, S., Feig, M.
Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model
JOURNAL OF PHYSICAL CHEMISTRY B, 110:548-556, JAN 12 2006
abstract, full text

Beevers, A.J., Kukol, A.
Conformational flexibility of the peptide hormone ghrelin in solution and lipid membrane bound: A molecular dynamics study
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 23:357-363, FEB 2006
abstract, full text

Vijayakrishnan, S., Qamra, R., Verma, C.S., Sen, R., Mande, S.C.
Cation-mediated interplay of loops in Chaperonin-10
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 23:365-375, FEB 2006
abstract, full text

Logadottir, A., Moses, P.G., Hinnemann, B., Topsoe, N.Y., Knudsen, K.G., Topsoe, H., Norskov, J.K.
A density functional study of inhibition of the HDS hydrogenation pathway by pyridine, benzene, and H2S on MoS2-based catalysts
CATALYSIS TODAY, 111:44-51, JAN 15 2006
abstract, full text

Matthews, J.F., Skopec, C.E., Mason, P.E., Zuccato, P., Torget, R.W., Sugiyama, J., Himmel, M.E., Brady, J.W.
Computer simulation studies of microcrystalline cellulose I beta
CARBOHYDRATE RESEARCH, 341:138-152, JAN 16 2006
abstract, full text

Noel, N., Flanagan, J., Kalko, S.G., Bajo, M.J.R., Manu, M.D., Fuster, J.L.G., Beutler, E., Corrons, J.L.V.
Two new phosphoglycerate kinase mutations associated with chronic haemolytic anaemia and neurological dysfunction in two patients from Spain
BRITISH JOURNAL OF HAEMATOLOGY, 132:523-529, FEB 2006
abstract, full text

Corry, B.
An energy-efficient gating mechanism in the acetylcholine receptor channel suggested by molecular and Brownian dynamics
BIOPHYSICAL JOURNAL, 90:799-810, FEB 2006
abstract, full text

Deol, S.S., Domene, C., Bond, P.J., Sansom, M.S.P.
Anionic phospholipid interactions with the potassium channel KcsA: Simulation studies
BIOPHYSICAL JOURNAL, 90:822-830, FEB 2006
abstract, full text

Lee, M.S., Olson, M.A.
Calculation of absolute protein-ligand binding affinity using path and endpoint approaches
BIOPHYSICAL JOURNAL, 90:864-877, FEB 2006
abstract, full text

Lim, R.Y.H., Aebi, U.
In silico access to the nuclear pore complex
STRUCTURE, 13:1741-1743, DEC 2005
full text

Murphy, G.E., Jensen, G.J.
Electron cryotomography of the E. coli pyruvate and 2-oxoglutarate dehydrogenase complexes
STRUCTURE, 13:1765-1773, DEC 2005
abstract, full text

Kass, I., Arkin, I.T.
How pH opens a H+ channel: The gating mechanism of influenza a M2
STRUCTURE, 13:1789-1798, DEC 2005
abstract, full text

Isgro, T.A., Schulten, K.
Binding dynamics of isolated nucleoporin repeat regions to importin-beta
STRUCTURE, 13:1869-1879, DEC 2005
abstract, full text

Marsella, L.
Modeling truncated hemoglobin vibrational dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 62:173-182, JAN 1 2006
abstract, full text

O'Donoghue, P., Sethi, A., Woese, C.R., Luthey-Schulten, Z.A.
The evolutionary history of Cys-tRNA(Cys) formation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:19003-19008, DEC 27 2005
abstract, full text

Rockwell, N.C., Lagarias, J.C.
The structure of phytochrome: A picture is worth a thousand spectra
PLANT CELL, 18:4-14, JAN 2006
full text

Kvamme, B., Kuznetsova, T., Aasoldsen, K.
Molecular simulations as a tool for selection of kinetic hydrate inhibitors
MOLECULAR SIMULATION, 31:1083-1094, DEC 2005
abstract, full text

Morizono, H., Woolston, J.E., Colombini, M., Tuchman, M.
The use of yeast mitochondria to study the properties of wild-type and mutant human mitochondrial ornithine transporter
MOLECULAR GENETICS AND METABOLISM, 86:431-440, DEC 2005
abstract, full text

Papaleo, E., Fantucci, P., Vai, M., De Gioia, L.
Three-dimensional structure of the catalytic domain of the yeast beta-(1,3)-glucan transferase Gas1: a molecular modeling investigation
JOURNAL OF MOLECULAR MODELING, 12:237-248, JAN 2006
abstract, full text

Shirran, S., Garnaud, P., Daff, S., McMillan, D., Barran, P.
The formation of a complex between calmodulin and neuronal nitric oxide synthase is determined by ESI-MS
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 2:465-476, DEC 22 2005
abstract, full text

Chakraborty, B., Doering, C.R., Goldburg, W.I.
Introduction: Ssecond Annual Gallery of Nonlinear images, Los Angeles, California, 2005.
CHAOS, 15: Art. No. 041101, DEC 2005
full text

Zhu, C., Lou, J.Z., McEver, R.P.
Catch bonds: Physical models, structural bases, biological function and rheological relevance
BIORHEOLOGY, 42:443-462, 2005
abstract, full text

Cruz, L., Urbanc, B., Borreguero, J.M., Lazo, N.D., Teplow, D.B., Stanley, H.E.
Solvent and mutation effects on the nucleation of amyloid beta-protein folding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:18258-18263, DEC 20 2005
abstract, full text

Beuning, P.J., Sawicka, D., Barsky, D., Walker, G.C.
Two processivity clamp interactions differentially alter the dual activities of UmuC
MOLECULAR MICROBIOLOGY, 59:460-474, JAN 2006
abstract, full text

Mason, P.E., Dempsey, C.E., Neilson, G.W., Brady, J.W.
Nanometer-scale ion aggregates in aqueous electrolyte solutions: Guanidinium sulfate and guanidinium thiocyanate
JOURNAL OF PHYSICAL CHEMISTRY B, 109:24185-24196, DEC 22 2005
abstract, full text

Chen, Z.J., Krause, G., Reif, B.
Structure and orientation of peptide inhibitors bound to beta-amyloid fibrils
JOURNAL OF MOLECULAR BIOLOGY, 354:760-776, DEC 9 2005
abstract, full text

Martin, J., Letellier, G., Marin, A., Taly, J.F., de Brevern, A.G., Gibrat, J.F.
Protein secondary structure assignment revisited: a detailed analysis of different assignment methods
BMC STRUCTURAL BIOLOGY, 5: Art. No. 17, SEP 15 2005
abstract, full text

Butu, A.
Performance analysis of parallel molecular dynamics simulation for biomolecular systems
JOURNAL OF OPTOELECTRONICS AND ADVANCED MATERIALS, 7:3101-3106, DEC 2005
abstract, full text

Smith, C.P., Thorsness, P.E.
Formation of an energized inner membrane in mitochondria with a gamma-deficient F-1-ATPase
EUKARYOTIC CELL, 4:2078-2086, DEC 2005
abstract, full text

Ribacka, C., Verkhovsky, M.I., Belevich, I., Bloch, D.A., Puustinen, A., Wikstrom, M.
An elementary reaction step of the proton pump is revealed by mutation of tryptophan-164 to phenylalanine in cytochrome c oxidase from Paracoccus denitrificans
BIOCHEMISTRY, 44:16502-16512, DEC 20 2005
abstract, full text

Hedin, E.M.K., Hoyrup, P., Patkar, S.A., Vind, J., Svendsen, A., Hult, K.
Implications of surface charge and curvature for the binding orientation of Thermomyces lanuginosus lipase on negatively charged or zwitterionic phospholipid vesicles as studied by ESR spectroscopy
BIOCHEMISTRY, 44:16658-16671, DEC 20 2005
abstract, full text

Herbert, J.M., Head-Gordon, M.
Accuracy and limitations of second-order many-body perturbation theory for predicting vertical detachment energies of solvated-electron clusters
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 8:68-78, 2006
abstract, full text

Yu, Z.Y., Jacobson, M.P., Friesner, R.A.
What role do surfaces play in GB models? A new-generation of surface-generalized Born model based on a novel Gaussian surface for biomolecules
JOURNAL OF COMPUTATIONAL CHEMISTRY, 27:72-89, JAN 15 2006
abstract, full text

Sourina, O., Korolev, N.
Visual mining and spatio-temporal querying in molecular dynamics
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 2:492-498, DEC 2005
abstract, full text

Benitez, B.A.S., Arora, K., Schlick, T.
In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism
BIOPHYSICAL JOURNAL, 90:42-56, JAN 2006
abstract, full text

Paramore, S., Ayton, G.S., Voth, G.A.
Extending a spectrin repeat unit. II: Rupture behavior
BIOPHYSICAL JOURNAL, 90:101-111, JAN 2006
abstract, full text

Friedman, R., Nachliel, E., Gutman, M.
Application of classical molecular dynamics for evaluation of proton transfer mechanism on a protein
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1710:67-77, DEC 20 2005
abstract, full text

Guo, W., Shi, L., Filizola, M., Weinstein, H., Javitch, J.A.
Crosstalk in G protein-coupled receptors: Changes at the transmembrane homodimer interface determine activation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:17495-17500, NOV 29 2005
abstract, full text

Salomonsson, L., Faxen, K., Adelroth, P., Brzezinski, P.
The timing of proton migration in membrane constituted cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:17624-17629, DEC 6 2005
abstract, full text

Bhardwaj, N., Langlois, R.E., Zhao, G.J., Lu, H.
Kernel-based machine learning protocol for predicting DNA-binding proteins
NUCLEIC ACIDS RESEARCH, 33:6486-6493, 2005
abstract, full text

Cymes, G.D., Ni, Y., Grosman, C.
Probing ion-channel pores one proton at a time
NATURE, 438:975-980, DEC 15 2005
abstract, full text

Horsman, G.P., Jirasek, A., Vaillancourt, F.H., Barbosa, C.J., Jarzecki, A.A., Xu, C.L., Mekmouche, Y., Spiro, T.G., Lipscomb, J.D., Blades, M.W., Turner, R.F.B., Eltis, L.D.
Spectroscopic studies of the anaerobic enzyme - Substrate complex of catechol 1,2-dioxygenase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127:16882-16891, DEC 7 2005
abstract, full text

Friedman, R., Nachliel, E., Gutman, M.
Protein surface dynamics: Interaction with water and small solutes
JOURNAL OF BIOLOGICAL PHYSICS, 31:433-452, DEC 2005
abstract, full text

Fiorin, G., Biekofsky, R.R., Pastore, A., Carloni, P.
Unwinding the helical linker of calcium-loaded calmodulin: A molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 61:829-839, DEC 1 2005
abstract, full text

Budi, A., Legge, F.S., Treutlein, H., Yarovsky, I.
Electric field effects on insulin chain-B conformation
JOURNAL OF PHYSICAL CHEMISTRY B, 109:22641-22648, DEC 1 2005
abstract, full text

Lissandron, V., Terrin, A., Collini, M., D'alfonso, L., Chirico, G., Pantano, S., Zaccolo, M.
Improvement of a FRET-based indicator for cAMP by linker design and stabilization of donor-acceptor interaction
JOURNAL OF MOLECULAR BIOLOGY, 354:546-555, DEC 2 2005
abstract, full text

Ryckelynck, M., Masquida, B., Giege, R., Frugier, M.
An intricate RNA structure with two tRNA-derived motifs directs complex formation between yeast aspartyl-tRNA synthetase and its mRNA
JOURNAL OF MOLECULAR BIOLOGY, 354:614-629, DEC 2 2005
abstract, full text

AbuKhader, M., Heap, J., De Matteis, C., Kellam, B., Doughty, S.W., Minton, N., Paoli, M.
Binding of the anticancer prodrug CB1954 to the activating enzyme NQO2 revealed by the crystal structure of their complex
JOURNAL OF MEDICINAL CHEMISTRY, 48:7714-7719, DEC 1 2005
abstract, full text

Bren, U., Hodoscek, M., Koller, J.
Development and validation of empirical force field parameters for netropsin
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 45:1546-1552, NOV-DEC 2005
abstract, full text

Carpena, X., Wiseman, B., Deemagarn, T., Singh, R., Switala, J., Ivancich, A., Fita, I., Loewen, P.C.
A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases
EMBO REPORTS, 6:1156-1162, DEC 2005
abstract, full text

Pinero, A., Villa, A., Vagt, T., Koksch, B., Mark, A.E.
A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations
BIOPHYSICAL JOURNAL, 89:3701-3713, DEC 2005
abstract, full text

Lee, H., Kandasamy, S.K., Larson, R.G.
Molecular dynamics simulations of the anchoring and tilting of the lung-surfactant peptide SP-B1-25 in palmitic acid monolayers
BIOPHYSICAL JOURNAL, 89:3807-3821, DEC 2005
abstract, full text

Cailliez, F., Lavery, R.
Cadherin mechanics and complexation: The importance of calcium binding
BIOPHYSICAL JOURNAL, 89:3895-3903, DEC 2005
abstract, full text

Petersen, F.N.R., Jensen, M.O., Nielsen, C.H.
Interfacial tryptophan residues: A role for the cation-pi effect?
BIOPHYSICAL JOURNAL, 89:3985-3996, DEC 2005
abstract, full text

Huang, C.Y., Balakrishnan, G., Spiro, T.G.
Early events in apomyoglobin unfolding probed by laser T-jump/UV resonance Raman spectroscopy
BIOCHEMISTRY, 44:15734-15742, DEC 6 2005
abstract, full text

Lasker, K., Dror, O., Nussinov, R., Wolfson, H.
Discovery of protein substructures in EM maps
ALGORITHMS IN BIOINFORMATICS, PROCEEDINGS, 3692:423-434, 2005
abstract, full text

Nadella, M., Bianchet, M.A., Gabelli, S.B., Barrila, J., Amzel, L.M.
Structure and activity of the axon guidance protein MICAL
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:16830-16835, NOV 15 2005
abstract, full text

Neyertz, S., Douanne, A., Brown, D.
Effect of interfacial structure on permeation properties of glassy polymers
MACROMOLECULES, 38:10286-10298, NOV 29 2005
abstract, full text

Savvin, S.N., Mazo, G.N., Ivanov-Schitz, A.K.
Oxygen diffusion in La2-xSrxCuO4-delta: Molecular dynamics study
DEFECTS AND DIFFUSION IN CERAMICS: AN ANNUAL RETROSPECTIVE VII, 242-244:27-42, 2005
abstract, full text

Campbell, N.H., Evans, D.A., Lee, M.P.H., Parkinson, G.N., Neidle, S.
Targeting the DNA minor groove with fused ring dicationic compounds: Comparison of in silico screening and a high-resolution crystal structure
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 16:15-19, JAN 1 2006
abstract, full text

Katti, D.R., Ghosh, P., Schmidt, S., Katti, K.S.
Mechanical properties of the sodium montmorillonite interlayer intercalated with amino acids
BIOMACROMOLECULES, 6:3276-3282, NOV-DEC 2005
abstract, full text

Luo, J., Bruice, T.C.
Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the base flipping
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:16194-16198, NOV 8 2005
abstract, full text

Imai, T., Hiraoka, R., Kovalenko, A., Hirata, F.
Water molecules in a protein cavity detected by a statistical-mechanical theory
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127:15334-15335, NOV 9 2005
full text

Rozhenko, A.B., Schoeller, W.W., Letzel, M.C., Decker, B., Agena, C., Mattay, J.
Conformational features of calix[4]arenes with alkali metal cations: A quantum chemical investigation with density functional theory
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 732:7-20, NOV 1 2005
abstract, full text

Verli, H., Guimaraes, J.A.
Insights into the induced fit mechanism in antithrombin-heparin interaction using molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 24:203-212, DEC 2005
abstract, full text

Habibian, R., Dzioba, J., Barrett, J., Galperin, M.Y., Loewen, P.C., Dibrov, P.
Functional analysis of conserved polar residues in Vc-NhaD, Na+/H+ antiporter of Vibrio cholerae
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:39637-39643, NOV 25 2005
abstract, full text

Biyani, M., Nishigaki, K.
Single-strand conformation polymorphism (SSCP) of oligodeoxyribonucleotides: An insight into solution structural dynamics of DNAs provided by gel electrophoresis and molecular dynamics simulations
JOURNAL OF BIOCHEMISTRY, 138:363-373, OCT 2005
abstract, full text

Papaleo, E., Fantucci, P., De Gioia, L.
Effects of calcium binding on structure and autolysis regulation in trypsins. A molecular dynamics investigation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 1:1286-1297, NOV-DEC 2005
abstract, full text

Sanbonmatsu, K.Y., Joseph, S., Tung, C.S.
Simulating movement of tRNA into the ribosome during decoding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:15854-15859, NOV 1 2005
abstract, full text

Fernandez, M.L., Marti, M.A., Crespo, A., Estrin, D.A.
Proximal effects in the modulation of nitric oxide synthase reactivity: a QM-MM study
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 10:595-604, OCT 2005
abstract, full text

Gaillard, C., Billard, I., Chaumont, A., Mekki, S., Ouadi, A., Denecke, M.A., Moutiers, G., Wipff, G.
Europium(III) and its halides in anhydrous room-temperature imidazolium-based ionic liquids: A combined TRES, EXAFS, and molecular dynamics study
INORGANIC CHEMISTRY, 44:8355-8367, NOV 14 2005
abstract, full text

Hosokawa, Y., Maki, S., Nagata, T.
Gold nanoparticles stabilized by tripod thioether oligomers: Synthesis and molecular dynamics studies
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN, 78:1773-1782, OCT 15 2005
abstract, full text

Grottesi, A., Domene, C., Hall, B., Sansom, M.S.P.
Conformational dynamics of M2 helices in KirBac channels: Helix flexibility in relation to gating via molecular dynamics simulations
BIOCHEMISTRY, 44:14586-14594, NOV 8 2005
abstract, full text

Streltsov, V.A., Carmichael, J.A., Nuttall, S.D.
Structure of a shark IgNAR antibody variable domain and modeling of an early-developmental isotype
PROTEIN SCIENCE, 14:2901-2909, NOV 2005
abstract, full text

Lemke, K., Wojciechowski, M., Laine, W., Bailly, C., Colson, P., Baginski, M., Larsen, A.K., Skladanowski, A.
Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities
NUCLEIC ACIDS RESEARCH, 33:6034-6047, 2005
abstract, full text

Lee, W.Y., Sine, S.M.
Principal pathway coupling agonist binding to channel gating in nicotinic receptors
NATURE, 438:243-247, NOV 10 2005
abstract, full text

Kumar, N.A., Seidel, C.
Polyelectrolyte brushes with added salt
MACROMOLECULES, 38:9341-9350, NOV 1 2005
abstract, full text

Buchete, N.V., Tycko, R., Hummer, G.
Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments
JOURNAL OF MOLECULAR BIOLOGY, 353:804-821, NOV 4 2005
abstract, full text

Case, D.A., Cheatham, T.E., Darden, T., Gohlke, H., Luo, R., Merz, K.M., Onufriev, A., Simmerling, C., Wang, B., Woods, R.J.
The Amber biomolecular simulation programs
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1668-1688, DEC 2005
abstract, full text

Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., Schulten, K.
Scalable molecular dynamics with NAMD
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1781-1802, DEC 2005
abstract, full text

Li, J.Q., Dai, Z.P., Jana, D., Callaway, D.J.E., Bu, Z.M.
Ezrin controls the macromolecular complexes formed between an adapter protein Na+/H+ exchanger regulatory factor and the cystic fibrosis transmembrane conductance regulator
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:37634-37643, NOV 11 2005
abstract, full text

Santiso, E.E., George, A.M., Turner, C.H., Kostov, M.K., Gubbins, K.E., Buongiorno-Nardelli, M., Sliwinska-Bartkowiak, M.
Adsorption and catalysis: The effect of confinement on chemical reactions
APPLIED SURFACE SCIENCE, 252:766-777, OCT 31 2005
abstract, full text

Kuo, A.L., Domene, C., Johnson, L.N., Doyle, D.A., Venien-Bryan, C.
Two different conformational states of the KirBac3.1 potassium channel revealed by electron crystallography
STRUCTURE, 13:1463-1472, OCT 2005
abstract, full text

Gorfe, A.A., Caflisch, A.
Functional plasticity in the substrate binding site of beta-secretase
STRUCTURE, 13:1487-1498, OCT 2005
abstract, full text

Freites, J.A., Tobias, D.J., von Heijne, G., White, S.H.
Interface connections of a transmembrane voltage sensor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:15059-15064, OCT 18 2005
abstract, full text

Little, R.J., Rodriguez, C.G.
Modeling of human corticosteroid binding globulin. Use of structure-activity relations in soft steroid binding to refine the structure
PHARMACEUTICAL RESEARCH, 22:1783-1792, NOV 2005
abstract, full text

Virnau, P., Kantor, Y., Kardar, M.
Knots in globule and Coll phases of a model polyethylene
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127:15102-15106, NOV 2 2005
abstract, full text

Liang, W.W., Zhou, M.
Pseudoelasticity of single crystalline Cu nanowires through reversible lattice reorientations
JOURNAL OF ENGINEERING MATERIALS AND TECHNOLOGY-TRANSACTIONS OF THE ASME, 127:423-433, OCT 2005
abstract, full text

Biswas, P.K., Gogonea, V.
A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical-molecular-mechanical calculations
JOURNAL OF CHEMICAL PHYSICS, 123: Art. No. 164114, OCT 22 2005
abstract, full text

Van Wynsberghe, A.W., Cui, Q.
Comparison of mode analyses at different resolutions applied to nucleic acid systems
BIOPHYSICAL JOURNAL, 89:2939-2949, NOV 2005
abstract, full text

Purhonen, P., Lundback, A.K., Lemonnier, R., Leblanc, G., Hebert, H.
Three-dimensional structure of the sugar symporter melibiose permease from cryo-electron microscopy
JOURNAL OF STRUCTURAL BIOLOGY, 152:76-83, OCT 2005
abstract, full text

Zhu, Q., Vaughn, M.W.
Surface tension effect on transmembrane channel stability in a model membrane
JOURNAL OF PHYSICAL CHEMISTRY B, 109:19474-19483, OCT 20 2005
abstract, full text

Clay, E.H., Gould, I.R.
A combined QM and MM investigation into guanine quadruplexes
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 24:138-146, OCT 2005
abstract, full text

Arkin, H.
Study of elastin sequences with solvent induced force field
INTERNATIONAL JOURNAL OF MODERN PHYSICS C, 16:1339-1346, SEP 2005
abstract, full text

Bennion, B.J., Cosman, M., Lightstone, F.C., Knize, M.G., Montgomery, J.L., Bennett, L.M., Felton, J.S., Kulp, K.S.
PhIP carcinogenicity in breast cancer: Computational and experimental evidence for competitive interactions with human estrogen receptor
CHEMICAL RESEARCH IN TOXICOLOGY, 18:1528-1536, OCT 2005
abstract, full text

Abild-Pedersen, F., Greeley, J., Norskov, J.K.
Understanding the effect of steps, strain, poisons, and alloying: Methane activation on Ni surfaces
CATALYSIS LETTERS, 105:9-13, NOV 2005
abstract, full text

Santiso, E.E., George, A.M., Sliwinska-Bartkowiak, M., Nardelli, M.B.
Effect of confinement on chemical reactions
ADSORPTION-JOURNAL OF THE INTERNATIONAL ADSORPTION SOCIETY, 11:349-354, 2005
abstract, full text

Greeley, J., Norskov, J.K.
A general scheme for the estimation of oxygen binding energies on binary transition metal surface alloys
SURFACE SCIENCE, 592:104-111, NOV 1 2005
abstract, full text

Ansari, S., Helms, V.
Statistical analysis of predominantly transient protein-protein interfaces
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 61:344-355, NOV 1 2005
abstract, full text

Liu, T.Y., Jenwitheesuk, E., Teller, D.C., Samudrala, R.
Structural insights into the cellular retinaldehyde-binding protein (CRALBP)
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 61:412-422, NOV 1 2005
abstract, full text

Chaumont, A., Schurhammer, R., Wipff, G.
Aqueous interfaces with hydrophobic room-temperature ionic liquids: A molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 109:18964-18973, OCT 13 2005
abstract, full text

Park, S., Radmer, R.J., Klein, T.E., Pande, V.S.
A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1612-1616, NOV 30 2005
abstract, full text

Arora, K., Beard, W.A., Wilson, S.H., Schlick, T.
Mismatch-induced conformational distortions in polymerase support an induced-fit mechanism for fidelity
BIOCHEMISTRY, 44:13328-13341, OCT 11 2005
abstract, full text

Wozniak, A.K., Nottrott, S., Kuhn-Holsken, E., Schroder, G.F., Grubmuller, H., Luhrmann, R., Seidel, C.A.M., Oesterhelt, F.
Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements
RNA-A PUBLICATION OF THE RNA SOCIETY, 11:1545-1554, OCT 2005
abstract, full text

Curcio, R., Caflisch, A., Paci, E.
Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex
PROTEIN SCIENCE, 14:2499-2514, OCT 2005
abstract, full text

Kazmirski, S.L., Zhao, Y.X., Bowman, G.D., O'Donnell, M., Kuriyan, J.
Out-of-plane motions in open sliding clamps: Molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:13801-13806, SEP 27 2005
abstract, full text

Frantsuzov, P.A., Mandelshtam, V.A.
Size-temperature phase diagram for small Lennard-Jones clusters
PHYSICAL REVIEW E, 72: Art. No. 037102, SEP 2005
abstract, full text

Alagona, G., Campanile, S., Ghio, C., Molin, D.
Is the bias introduced in a FEP calculation by parameterizing a QM reaction acceptable? Comparison with Car-Parrinello MD/AMBER results for the second proton transfer in triosephosphate isomerase (TIM)
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 729:131-139, SEP 16 2005
abstract, full text

Maragakis, P., Karplus, M.
Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
JOURNAL OF MOLECULAR BIOLOGY, 352:807-822, SEP 30 2005
abstract, full text

Kondou, Y., Kitazawa, D., Takeda, S., Tsuchiya, Y., Yamashita, E., Mizuguchi, M., Kawano, K., Tsukihara, T.
Structure of the central hub of bacteriophage Mu baseplate determined by X-ray crystallography of gp44
JOURNAL OF MOLECULAR BIOLOGY, 352:976-985, SEP 30 2005
abstract, full text

Wibowo, F.R., Rauch, C., Trieb, M., Liedl, K.R.
M.TaqI facilitates the base flipping via an unusual DNA backbone conformation
BIOPOLYMERS, 79:128-138, OCT 15 2005
abstract, full text

Amzel, L.M., Siebert, X., Armstrong, A., Pabon, G.
Thermodynamic calculations in biological systems
BIOPHYSICAL CHEMISTRY, 117:239-254, OCT 3 2005
abstract, full text

Delmas, J., Robin, F., Bittar, F., Chanal, C., Bonnet, R.
Unexpected enzyme TEM-126: Role of mutation Asp179Glu
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 49:4280-4287, OCT 2005
abstract, full text

Stefankova, P., Maderova, J., Barak, I., Kollarova, M., Otwinowski, Z.
Expression, purification and X-ray crystallographic analysis of thioredoxin from Streptomyces coelicolor
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 61:164-168, FEB 2005
full text

Cohen, J., Kim, K., King, P., Seibert, M., Schulten, K.
Finding gas diffusion pathways in proteins: Application to O-2 and H-2 transport in Cpl [FeFe]-hydrogenase and the role of packing defects
STRUCTURE, 13:1321-1329, SEP 2005
abstract, full text

Redmond, T.M., Poliakov, E., Yu, S., Tsai, J.Y., Lu, Z.J., Gentleman, S.
Mutation of key residues of RPE65 abolishes its enzymatic role as isomerohydrolase in the visual cycle
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:13658-13663, SEP 20 2005
abstract, full text

Kostov, M.K., Santiso, E.E., George, A.M., Gubbins, K.E., Nardelli, M.B.
Dissociation of water on defective carbon substrates
PHYSICAL REVIEW LETTERS, 95: Art. No. 136105, SEP 23 2005
abstract, full text

Schwarzl, S.M., Smith, J.C., Kaina, B., Efferth, T.
Molecular modeling of O-6-methylguanine-DNA methyltransferase mutant proteins encoded by single nucleotide polymorphisms
INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE, 16:553-557, OCT 2005
abstract, full text

Olkhova, E., Helms, V., Michel, H.
Titration behavior of residues at the entrance of the D-pathway of cytochrome c oxidase from Paracoccus denitrificans investigated by continuum electrostatic calculations
BIOPHYSICAL JOURNAL, 89:2324-2331, OCT 2005
abstract, full text

Yonkunas, M.J., Xu, Y., Tang, P.
Anesthetic interaction with ketosteroid isomerase: Insights from molecular dynamics simulations
BIOPHYSICAL JOURNAL, 89:2350-2356, OCT 2005
abstract, full text

Lemaitre, V., Yeagle, P., Watts, A.
Molecular dynamics simulations of retinal in rhodopsin: From the dark-adapted state towards lumirhodopsin
BIOCHEMISTRY, 44:12667-12680, SEP 27 2005
abstract, full text

Han, D., Morgan, J.E., Gennis, R.B.
G204D, a mutation that blocks the proton-conducting D-channel of the aa(3)-type cytochrome c oxidase from Rhodobacter sphaeroides
BIOCHEMISTRY, 44:12767-12774, SEP 27 2005
abstract, full text

Jin, L., Barran, P.E., Deakin, J.A., Lyon, M., Uhrin, D.
Conformation of glycosaminoglycans by ion mobility mass spectrometry and molecular modelling
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 7:3464-3471, 2005
abstract, full text

Siegmund, K., Maheshwary, S., Narayanan, S., Connors, W., Riedrich, M., Printz, M., Richert, C.
Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it
NUCLEIC ACIDS RESEARCH, 33:4838-4848, 2005
abstract, full text

Trzaskowski, B., Leonarski, F., Les, A., Adamowicz, L.
Modeling tubulin at interfaces. Immobilization of microtubules on self-assembled monolayers
JOURNAL OF PHYSICAL CHEMISTRY B, 109:17734-17742, SEP 22 2005
abstract, full text

Gal, P., Harmat, V., Kocsis, A., Bian, T., Barna, L., Ambrus, G., Vegh, B., Balczer, J., Sim, R.B., Naray-Szabo, G., Zavodszky, P.
A true autoactivating enzyme - Structural insight into mannose-binding lectin-associated serine protease-2 activations
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:33435-33444, SEP 30 2005
abstract, full text

Jolley, C., Ben-Shem, A., Nelson, N., Fromme, P.
Structure of plant photosystem I revealed by theoretical modeling
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:33627-33636, SEP 30 2005
abstract, full text

Tuszynski, J.A., Luchko, T., Portet, S., Dixon, J.M.
Anisotropic elastic properties of microtubules
EUROPEAN PHYSICAL JOURNAL E, 17:29-35, MAY 2005
abstract, full text

Pan, W.L., Tan, N.H., Zeng, G.Z., Zhang, Y.M., Jia, R.R.
Amentoflavone and its derivatives as novel natural inhibitors of human Cathepsin B
BIOORGANIC & MEDICINAL CHEMISTRY, 13:5819-5825, OCT 15 2005
abstract, full text

Andre, S., Siebert, H.C., Nishiguchi, M., Tazaki, K., Gabius, H.J.
Evidence for lectin activity of a plant receptor-like protein kinase by application of neoglycoproteins and bioinformatic algorithms
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1725:222-232, SEP 15 2005
abstract, full text

Chu, J.W., Voth, G.A.
Allostery of actin filaments: Molecular dynamics simulations and coarse-grained analysis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:13111-13116, SEP 13 2005
abstract, full text

Thorpe, I.F., Brooks, C.L.
Conformational substates modulate hydride transfer in dihydrofolate reductase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127:12997-13006, SEP 21 2005
abstract, full text

Arora, G., Klauda, J.B., Sandler, S.I.
A comparative study of nitrogen physisorption on different C-70 crystal structures using an ab initio based potential
JOURNAL OF PHYSICAL CHEMISTRY B, 109:17267-17273, SEP 15 2005
abstract, full text

Johansson, T., Oswald, C., Pedersen, A., Tornroth, S., Okvist, M., Karlsson, B.G., Rydstrom, J., Krengel, U.
X-ray structure of domain I of the proton-pumping membrane protein transhydrogenase from Escherichia coli
JOURNAL OF MOLECULAR BIOLOGY, 352:299-312, SEP 16 2005
abstract, full text

Lee, J.E., Smith, G.D., Horvatin, C., Huang, D.J.T., Cornell, K.A., Riscoe, M.K., Howell, P.L.
Structural snapshots of MTA/AdoHcy nucleosidase along the reaction coordinate provide insights into enzyme and nucleoside flexibility during catalysis
JOURNAL OF MOLECULAR BIOLOGY, 352:559-574, SEP 23 2005
abstract, full text

Bennetts, B., Rychkov, G.Y., Ng, H.L., Morton, C.J., Stapleton, D., Parker, M.W., Cromer, B.A.
Cytoplasmic ATP-sensing domains regulate gating of skeletal muscle ClC-1 chloride channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:32452-32458, SEP 16 2005
abstract, full text

Rovira, C.
Structure, protonation state and dynamics of catalase compound II
CHEMPHYSCHEM, 6:1820-1826, SEP 5 2005
abstract, full text

Noto, R., Martorana, V., Bulone, D., San Biagio, P.L.
Role of charges and solvent on the conformational properties of poly(galacturonic acid) chains: A molecular dynamics study
BIOMACROMOLECULES, 6:2555-2562, SEP-OCT 2005
abstract, full text

Myers, R.S., Amaro, R.E., Luthey-Schulten, Z.A., Davisson, V.J.
Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase
BIOCHEMISTRY, 44:11974-11985, SEP 13 2005
abstract, full text

Tapley, T.L., Cupp-Vickery, J.R., Vickery, L.E.
Sequence-dependent peptide binding orientation by the molecular chaperone DnaK
BIOCHEMISTRY, 44:12307-12315, SEP 20 2005
abstract, full text

Czekster, R.M., de Souza, O.N.
VIZ - A graphical open-source architecture for use in structural bioinformatics
ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, PROCEEDINGS, 3594:226-229, 2005
abstract, full text

Satchell, J.F., Malby, R.L., Luo, C.S., Adisa, A., Alpyurek, A.E., Klonis, N., Smith, B.J., Tilley, L., Colman, P.M.
Structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 61:1213-1221, SEP 2005
abstract, full text

Mathe, J., Aksimentiev, A., Nelson, D.R., Schulten, K., Meller, A.
Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:12377-12382, AUG 30 2005
abstract, full text

Fowler, P.W., Jha, S., Coveney, P.V.
Grid-based steered thermodynamic integration accelerates the calculation of binding free energies
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1999-2015, AUG 15 2005
abstract, full text

Giordanetto, F., Fowler, P.W., Saqi, M., Coveney, P.V.
Large scale molecular dynamics simulation of native and mutant dihydropteroate synthase-sulphanilamide complexes suggests the molecular basis for dihydropteroate synthase drug resistance
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2055-2073, AUG 15 2005
abstract, full text

Rousay, E.R., Fu, H.C., Robinson, J.M., Essex, J.W., Frey, J.G.
Grid-based dynamic electronic publication: a case study using combined experiment and simulation studies of crown ethers at the air/water interface
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2075-2095, AUG 15 2005
abstract, full text

Spaar, A., Helms, V.
Free energy landscape of protein-protein encounter resulting from Brownian dynamics simulations of Barnase : Barstar
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 1:723-736, JUL-AUG 2005
abstract, full text

Anishkin, A., Kung, C.
Microbial mechanosensation
CURRENT OPINION IN NEUROBIOLOGY, 15:397-405, AUG 2005
abstract, full text

Wang, Y., Schulten, K., Tajkhorshid, E.
What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF
STRUCTURE, 13:1107-1118, AUG 2005
abstract, full text

Holm, M.M., Lunn, M.L., Traynelis, S.F., Kastrup, J.S., Egebjerg, J.
Structural determinants of agonist-specific kinetics at the ionotropic glutamate receptor 2
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:12053-12058, AUG 23 2005
abstract, full text

Habtemariam, B., Anisimov, V.M., MacKerell, A.D.
Cooperative binding of DNA and CBF beta to the Runt domain of the CBF alpha studied via MD simulations
NUCLEIC ACIDS RESEARCH, 33:4212-4222, 2005
abstract, full text

Faxen, K., Gilderson, G., Adelroth, P., Brzezinski, P.
A mechanistic principle for proton pumping by cytochrome c oxidase
NATURE, 437:286-289, SEP 8 2005
abstract, full text

Neugebauer, J., Jacob, C.R., Wesolowski, T.A., Baerends, E.J.
An explicit quantum chemical method for modeling large solvation shells applied to aminocoumarin C151
JOURNAL OF PHYSICAL CHEMISTRY A, 109:7805-7814, SEP 1 2005
abstract, full text

Krishnamoorthy, G., Shi, J.Y., Sept, D., Cui, J.M.
The NH2 terminus of RCK1 domain regulates Ca2+-dependent BKCa channel gating
JOURNAL OF GENERAL PHYSIOLOGY, 126:227-241, SEP 2005
abstract, full text

Bae, E., Phillips, G.N.
Identifying and engineering ion pairs in adenylate kinases
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:30943-30948, SEP 2 2005
abstract, full text

McNally, D.J., Jarrell, H.C., Li, J., Khieu, N.H., Vinogradov, E., Szymanski, C.M., Brisson, J.R.
The HS : 1 serostrain of Campylobacter jejuni has a complex teichoic acid-like capsular polysaccharide with nonstoichiometric fructofuranose branches and O-methyl phosphoramidate groups
FEBS JOURNAL, 272:4407-4422, SEP 2005
abstract, full text

White, S.H., von Heijne, G.
Transmembrane helices before, during, and after insertion
CURRENT OPINION IN STRUCTURAL BIOLOGY, 15:378-386, AUG 2005
abstract, full text

Trylska, J., Tozzini, V., McCammon, J.A.
Exploring global motions and correlations in the ribosome
BIOPHYSICAL JOURNAL, 89:1455-1463, SEP 2005
abstract, full text

Sener, M.K., Jolley, C., Ben-Shem, A., Fromme, P., Nelson, N., Croce, R., Schulten, K.
Comparison of the light-harvesting networks of plant and cyanobacterial photosystem I
BIOPHYSICAL JOURNAL, 89:1630-1642, SEP 2005
abstract, full text

Cheng, M.H.Y., Cascio, M., Coalson, R.D.
Theoretical studies of the M2 transmembrane segment of the glycine receptor: Models of the open pore structure and current-voltage characteristics
BIOPHYSICAL JOURNAL, 89:1669-1680, SEP 2005
abstract, full text

Jensen, M.O., Rothlisberger, U., Rovira, C.
Hydroxide and proton migration in aquaporins
BIOPHYSICAL JOURNAL, 89:1744-1759, SEP 2005
abstract, full text

Martinez, L., Sonoda, M.T., Webb, P., Baxter, J.D., Skaf, M.S., Polikarpov, I.
Molecular dynamics simulations reveal multiple pathways of ligand dissociation from thyroid hormone receptors
BIOPHYSICAL JOURNAL, 89:2011-2023, SEP 2005
abstract, full text

Donald, J.E., Shakhnovich, E.I.
Predicting specificity-determining residues in two large eukaryotic transcription factor families
NUCLEIC ACIDS RESEARCH, 33:4455-4465, 2005
abstract, full text

Schmidt, S.R., Katti, D.R., Ghosh, P., Katti, K.S.
Evolution of mechanical response of sodium montmorillonite interlayer with increasing hydration by molecular dynamics
LANGMUIR, 21:8069-8076, AUG 16 2005
abstract, full text

Zhang, J., Xu, Y.C., Shen, J.H., Luo, X.M., Chen, J.G., Chen, K.X., Zhu, W.L., Jiang, H.L.
Dynamic mechanism for the autophosphorylation of CheA histidine kinase: Molecular dynamics simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127:11709-11719, AUG 24 2005
abstract, full text

Krasovska, M.V., Sefcikova, J., Spackova, N., Sponer, J., Walter, N.G.
Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations
JOURNAL OF MOLECULAR BIOLOGY, 351:731-748, AUG 26 2005
abstract, full text

Jung, G., Ma, Y.Z., Prall, B.S., Fleming, G.R.
Ultrafast fluorescence depolarisation in the yellow fluorescent protein due to its dimerisation
CHEMPHYSCHEM, 6:1628-1632, AUG 12 2005
abstract, full text

Mulkidjanian, A.Y.
Ubiquinol oxidation in the cytochrome bc(1) complex: Reaction mechanism and prevention of short-circuiting
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1709:5-34, AUG 15 2005
abstract, full text

Hemp, J., Christian, C., Barquera, B., Gennis, R.B., Martinez, T.J.
Helix switching of a key active-site residue in the cytochrome cbb(3) oxidases
BIOCHEMISTRY, 44:10766-10775, AUG 16 2005
abstract, full text

Secundo, F., Russo, C., Giordano, A., Carrea, G., Rossi, M., Raia, C.A.
Temperature-induced conformational change at the catalytic site of Sulfolobus solfataricus alcohol dehydrogenase highlighted by Asn249Tyr substitution. A hydrogen/deuterium exchange, kinetic, and fluorescence quenching study
BIOCHEMISTRY, 44:11040-11048, AUG 23 2005
abstract, full text

Lee, J.E., Luong, W., Huang, D.J.T., Cornell, K.A., Riscoe, M.K., Howell, P.L.
Mutational analysis of a nucleosidase involved in quorum-sensing autoinducer-2 biosynthesis
BIOCHEMISTRY, 44:11049-11057, AUG 23 2005
abstract, full text

Aci, S., Mazier, S., Genest, D.
Conformational pathway for the kissing complex - Extended dimer transition of the SL1 stem-loop from genomic HIV-1 RNA as monitored by targeted molecular dynamics techniques
JOURNAL OF MOLECULAR BIOLOGY, 351:520-530, AUG 19 2005
abstract, full text

Jason, D., Metzger, R.P., Brownlee, R.T.C., Ng, C.A., Bergdahl, M., Separovic, F.
The conformational flexibility of the antibiotic virginiamycin M-1
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 34:383-388, JUL 2005
abstract, full text

Porter, C.J., Wilce, M.C.J., Mackay, J.P., Leedman, P., Wilce, J.A.
Grb7-SH2 domain dimerisation is affected by a single point mutation
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 34:454-460, JUL 2005
abstract, full text

Pirc, E.T., Zidar, J., Bukovec, P., Hodoscek, M.
Molecular modeling of cobalt(II) hyaluronate
CARBOHYDRATE RESEARCH, 340:2064-2069, SEP 5 2005
abstract, full text

Trylska, J., McCammon, J.A., Brooks, C.L.
Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127:11125-11133, AUG 10 2005
abstract, full text

Branden, G., Branden, M., Schmidt, B., Mills, D.A., Ferguson-Miller, S., Brzezinski, P.
The protonation state of a heme propionate controls electron transfer in cytochrome c oxidase
BIOCHEMISTRY, 44:10466-10474, AUG 9 2005
abstract, full text

Ourliac-Garnier, I., Elizondo-Riojas, M.A., Redon, S., Farrell, N.P., Bombard, S.
Cross-links of quadruplex structures from human telomeric DNA by dinuclear platinum complexes show the flexibility of both structures
BIOCHEMISTRY, 44:10620-10634, AUG 9 2005
abstract, full text

Wikstrom, M., Ribacka, C., Molin, M., Laakkonen, L., Verkhovsky, M., Puustinen, A.
Gating of proton and water transfer in the respiratory enzyme cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:10478-10481, JUL 26 2005
abstract, full text

Ferrando, R., Andrei, M., Relini, A., Rolandi, R., Gliozzi, A.
Molecular dynamics simulations of the indentation of a crystalline surface by an atomic force microscope tip
PHYSICAL REVIEW B, 72: Art. No. 045412, JUL 2005
abstract, full text

Xiang, T.X., Anderson, B.D.
Distribution and effect of water content on molecular mobility in poly(vinylpyrrolidone) glasses: A molecular dynamics simulation
PHARMACEUTICAL RESEARCH, 22:1205-1214, AUG 2005
abstract, full text

Patel, R.Y., Balaji, P.V.
Effect of the choice of the pressure coupling method on the spontaneous aggregation of DPPC molecules
JOURNAL OF PHYSICAL CHEMISTRY B, 109:14667-14674, AUG 4 2005
abstract, full text

Ahumada, H., Montecinos, R., Tieleman, D.P., Weiss-Lopez, B.E.
Orientation and dynamics of benzyl alcohol and benzyl alkyl ethers dissolved in nematic lyotropic liquid crystals. H-2 NMR and molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 109:6644-6651, AUG 4 2005
abstract, full text

Melville, J.L., Lovelock, K.R.J., Wilson, C., Allbutt, B., Burke, E.K., Lygo, B., Hirst, J.D.
Exploring phase-transfer catalysis with molecular dynamics and 3D/4D quantitative structure-selectivity relationships
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 45:971-981, JUL-AUG 2005
abstract, full text

Damjanovic, A., Garcia-Moreno, B., Lattman, E.E., Garcia, A.E.
Molecular dynamics study of water penetration in staphylococcal nuclease
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 60:433-449, AUG 15 2005
abstract, full text

Zhao, Q., Nagaswamy, U., Lee, H., Xia, Y.L., Huang, H.C., Gao, X.L., Fox, G.E.
NMR structure and Mg2+ binding of an RNA segment that underlies the L7/L12 stalk in the E.coli 50S ribosomal subunit
NUCLEIC ACIDS RESEARCH, 33:3145-3153, 2005
abstract, full text

Cojocaru, V., Klement, R., Jovin, T.M.
Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif
NUCLEIC ACIDS RESEARCH, 33:3435-3446, 2005
abstract, full text

Malek, K., Odijk, T., Coppens, M.O.
Diffusion of water and sodium counter-ions in nanopores of a beta-lactoglobulin crystal: a molecular dynamics study
NANOTECHNOLOGY, 16:S522-S530, JUL 2005
abstract, full text

Sharma, G., Badescu, M., Dubey, A., Mavroidis, C., Tomassone, S.M., Yarmush, M.L.
Kinematics and workspace analysis of protein based nano-actuators
JOURNAL OF MECHANICAL DESIGN, 127:718-727, JUL 2005
abstract, full text

Friedman, R., Nachliel, E., Gutman, M.
Molecular dynamics of a protein surface: Ion-residues interactions
BIOPHYSICAL JOURNAL, 89:768-781, AUG 2005
abstract, full text

Caballero-Herrera, A., Nordstrand, K., Berndt, K.D., Nilsson, L.
Effect of urea on peptide conformation in water: Molecular dynamics and experimental characterization
BIOPHYSICAL JOURNAL, 89:842-857, AUG 2005
abstract, full text

Katsarou, M.E., Papakyriakou, A., Katsaros, N., Scorilas, A.
Expression of the C-terminal domain of novel human SR-A1 protein: Interaction with the CTD domain of RNA polymerase II
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 334:61-68, AUG 19 2005
abstract, full text

Choudhary, M.I., Nawaz, S.A., Z.a.h.e.e.r.-.u.l.-.H.a.q., Lodhi, M.A., Ghayur, M.N., Jalil, S., Riaz, N., Yousuf, S., Malik, A., Gilani, A.H., A.t.t.a.-.u.r.-.R.a.h.m.a.n.
Withanolides, a new class of natural cholinesterase inhibitors with calcium antagonistic properties
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 334:276-287, AUG 19 2005
abstract, full text

Beckstein, O., Sansom, M.S.P.
The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores
PHYSICAL BIOLOGY, 1:42-52, JUN 2004
abstract, full text

Elber, R.
Computer simulations of protein folding: Classical trajectories by optimization of action
COMPUTER PHYSICS COMMUNICATIONS, 169:277-283, JUL 1 2005
abstract, full text

Browne, W.R., O'Boyle, N.M., McGarvey, J.J., Vos, J.G.
Elucidating excited state electronic structure and intercomponent interactions in multicomponent and supramolecular systems
CHEMICAL SOCIETY REVIEWS, 34:641-663, 2005
abstract, full text

Roccatano, D., Wong, T.S., Schwaneberg, U., Zacharias, M.
Structural and dynamic properties of cytochrome P450BM-3 in pure water and in a dimethylsulfoxide/water mixture
BIOPOLYMERS, 78:259-267, AUG 5 2005
abstract, full text

Zamolodchikova, T.S., Smirnova, E.V., Andrianov, A.N., Kashparov, I.V., Kotsareva, O.D., Sokolova, E.A., Ignatov, K.B., Pemberton, A.D.
Cloning and molecular modeling of duodenase with respect to evolution of substrate specificity within mammalian serine proteases that have lost a conserved active-site disulfide bond
BIOCHEMISTRY-MOSCOW, 70:672-684, JUN 2005
abstract, full text

Plassmeyer, M.L., Soldan, S.S., Stachelek, K.M., Martin-Garcia, J., Gonzalez-Scarano, F.
California serogroup, GC (Gl) glycoprotein is the principal determinant of pH-dependent cell fusion and entry
VIROLOGY, 338:121-132, JUL 20 2005
abstract, full text

Izaguirre, J.A., Hampton, S.S., Matthey, T.
Parallel multigrid summation for the N-body problem
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 65:949-962, AUG 2005
abstract, full text

Stan, G., Brooks, B.R., Thirumalai, D.
Probing the "annealing" mechanism of GroEL mini-chaperone using molecular dynamics simulations
JOURNAL OF MOLECULAR BIOLOGY, 350:817-829, JUL 22 2005
abstract, full text

Choe, S., Sun, S.X.
The elasticity of alpha-helices
JOURNAL OF CHEMICAL PHYSICS, 122: Art. No. 244912, JUN 22 2005
abstract, full text

Wang, G.L., Yamasaki, K., Daiho, T., Suzuki, H.
Critical hydrophobic interactions between phosphorylation and actuator domains of Ca2+-ATPase for hydrolysis of phosphorylated intermediate
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:26508-26516, JUL 15 2005
abstract, full text

Allis, D.G., Drexler, K.E.
Design and analysis of a molecular tool for carbon transfer in mechanosynthesis
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 2:45-55, MAR 2005
abstract, full text

Fernandez, L.E., Perez, C., Segovia, L., Rodriguez, M.H., Gill, S.S., Bravo, A., Soberon, M.
Cry11Aa toxin from Bacillus thuringiensis binds its receptor in Aedes aegypti mosquito larvae through loop alpha-8 of domain II
FEBS LETTERS, 579:3508-3514, JUL 4 2005
abstract, full text

Jenkins, J., Sengupta, D., Sundaram, S.
Characterization of a solid state DNA nanopore sequencer using multi-scale (nano-to-device) modeling
COMPUTATIONAL SCIENCE - ICCS 2005, PT 3, 3516:309-316, 2005
abstract, full text

Shi, X.H., Yong, K., Zhao, Y.P., Gao, H.J.
Molecular dynamics simulation of peeling a DNA molecule on substrate
ACTA MECHANICA SINICA, 21:249-256, JUN 2005
abstract, full text

Smith, G.R., Fitzjohn, P.W., Page, C.S., Bates, P.A.
Incorporation of flexibility into rigid-body docking: Applications in rounds 3-5 of CAPRI
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 60:263-268, AUG 1 2005
abstract, full text

Mezzenga, R., Grigorov, M., Zhang, Z.D., Servais, C., Sagalowicz, L., Romoscanu, A.I., Khanna, V., Meyer, C.
Polysaccharide-induced order-to-order transitions in lyotropic liquid crystals
LANGMUIR, 21:6165-6169, JUL 5 2005
abstract, full text

Dittrich, M., Freddolino, P.L., Schulten, K.
When light falls in LOV: A quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii
JOURNAL OF PHYSICAL CHEMISTRY B, 109:13006-13013, JUL 7 2005
abstract, full text

Kvamme, B., Kuznetsova, T., Aasoldsen, K.
Molecular dynamics simulations for selection of kinetic hydrate inhibitors
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 23:524-536, JUN 2005
abstract, full text

van Vlijmen, H.W.T., Karplus, M.
Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry
JOURNAL OF MOLECULAR BIOLOGY, 350:528-542, JUL 15 2005
abstract, full text

Yamaguchi, A., Tada, T., Wada, K., Nakaniwa, T., Kitatani, T., Sogabe, Y., Takao, M., Sakai, T., Nishimura, K.
Structural basis for thermostability of endo-1,5-alpha-L-arabinanase from Bacillus thermodenitrificans TS-3
JOURNAL OF BIOCHEMISTRY, 137:587-592, MAY 2005
abstract, full text

Punta, M., Rost, B.
PROFcon: novel prediction of long-range contacts
BIOINFORMATICS, 21:2960-2968, JUL 1 2005
abstract, full text

Barrett, C.P., Noble, M.E.M.
Dynamite extended: two new services to simplify protein dynamic analysis
BIOINFORMATICS, 21:3174-3175, JUL 15 2005
abstract, full text

Bisset, D., Corry, B., Chung, S.H.
The fast gating mechanism in CIC-0 channels
BIOPHYSICAL JOURNAL, 89:179-186, JUL 2005
abstract, full text

Amaro, R.E., Myers, R.S., Davisson, V.J., Luthey-Schulten, Z.A.
Structural elements in IGP synthase exclude water to optimize ammonia transfer
BIOPHYSICAL JOURNAL, 89:475-487, JUL 2005
abstract, full text

Polfer, N.C., Haselmann, K.F., Langridge-Smith, P.R.R., Barran, P.E.
Structural investigation of naturally occurring peptides by electron capture dissociation and AMBER force field modelling
MOLECULAR PHYSICS, 103:1481-1489, JUN 10 2005
abstract, full text

Branduardi, D., Gervasio, F.L., Cavalli, A., Recanatini, M., Parrinello, M.
The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127:9147-9155, JUN 29 2005
abstract, full text

Ray, W.K., Keith, S.M., DeSantis, A.M., Hunt, J.P., Larson, T.J., Helm, R.F., Kennelly, P.J.
A phosphohexomutase from the archaeon Sulfolobus solfataricus is covalently modified by phosphorylation on serine
JOURNAL OF BACTERIOLOGY, 187:4270-4275, JUN 2005
abstract, full text

Giordano, A., Febbraio, F., Russo, C., Rossi, M., Raia, C.A.
Evidence for co-operativity in coenzyme binding to tetrameric Sulfolobus solfataricus alcohol dehydrogenase and its structural basis: fluorescence, kinetic and structural studies of the wild-type enzyme and non-co-operative N249Y mutant
BIOCHEMICAL JOURNAL, 388:657-667, JUN 1 2005
abstract, full text

Choudhary, M.I., Nawaz, S.A., Z.a.h.e.e.r.-.u.l.-.H.a.q., Azim, M.K., Ghayur, M.N., Lodhi, M.A., Jalil, S., Khalid, A., Ahmed, A., Rode, B.M., A.t.t.a.-.u.r.-.R.a.h.m.a.n., Gilani, A.U.H., Ahmad, V.U.
Juliflorine: A potent natural peripheral anionic-site-binding inhibitor of acetylcholinesterase with calcium-channel blocking potential, a leading candidate for Alzheimer's disease therapy
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 332:1171-1179, JUL 15 2005
abstract, full text

Fleming, S., Rohl, A.
GDIS: a visualization program for molecular and periodic systems
ZEITSCHRIFT FUR KRISTALLOGRAPHIE, 220:580-584, 2005
abstract, full text

Valle, M.
STM3: a chemistry visualization platform
ZEITSCHRIFT FUR KRISTALLOGRAPHIE, 220:585-588, 2005
abstract, full text

Henin, J., Pohorille, A., Chipot, C.
Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127:8478-8484, JUN 15 2005
abstract, full text

Herbert, J.M., Head-Gordon, M.
Calculation of electron detachment energies for water cluster anions: An appraisal of electronic structure methods, with application to (H2O)(20)over-bar and (H2O)(24)over-bar
JOURNAL OF PHYSICAL CHEMISTRY A, 109:5217-5229, JUN 16 2005
abstract, full text

Galstyan, A.S., Zaric, S.D., Knapp, E.W.
Computational studies on imidazole heme conformations
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 10:343-354, JUN 2005
abstract, full text

Tsai, H.H., Reches, M., Tsai, C.J., Gunasekaran, K., Gazit, E., Nussinov, R.
Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:8174-8179, JUN 7 2005
abstract, full text

Dlugosz, M., Antosiewicz, J.M.
The impact of protonation equilibria on protein structure
JOURNAL OF PHYSICS-CONDENSED MATTER, 17:S1607-S1616, MAY 11 2005
abstract, full text

Orzechowski, M., Cieplak, P.
Application of steered molecular dynamics (SMD) to study DNA-drug complexes and probing helical propensity of amino acids
JOURNAL OF PHYSICS-CONDENSED MATTER, 17:S1627-S1640, MAY 11 2005
abstract, full text

Mezer, A., Friedman, R., Noivirt, O., Nachliel, E., Gutman, M.
The mechanism of proton transfer between adjacent sites exposed to water
JOURNAL OF PHYSICAL CHEMISTRY B, 109:11379-11388, JUN 9 2005
abstract, full text

Crocker, M.S., Hampton, S.S., Matthey, T., Izaguirre, J.A.
MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1021-1031, JUL 30 2005
abstract, full text

Chiu, H.C., Chang, C.A., Hu, Y.J.
Prediction of orthologous relationship by functionally important sites
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, 78:209-222, JUN 2005
abstract, full text

Law, M.J., Chambers, E.J., Katsamba, P.S., Haworth, I.S., Laird-Offringa, I.A.
Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction
NUCLEIC ACIDS RESEARCH, 33:2917-2928, 2005
abstract, full text

Litjens, S.H.M., Wilhelmsen, K., de Pereda, J.M., Perrakis, A., Sonnenberg, A.
Modeling and experimental validation of the binary complex of the plectin actin-binding domain and the first pair of fibronectin type III (FNIII) domains of the beta 4 integrin
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:22270-22277, JUN 10 2005
abstract, full text

Aksimentiev, A., Schulten, K.
Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map
BIOPHYSICAL JOURNAL, 88:3745-3761, JUN 2005
abstract, full text

Liu, Z.W., Xu, Y., Tang, P.
Molecular dynamics Simulations of C2F6 effects on gramicidin A: Implications of the mechanisms of general anesthesia
BIOPHYSICAL JOURNAL, 88:3784-3791, JUN 2005
abstract, full text

Nielsen, S.O., Ensing, B., Ortiz, V., Moore, P.B., Klein, M.L.
Lipid bilayer perturbations around a transmembrane nanotube: A coarse grain molecular dynamics study
BIOPHYSICAL JOURNAL, 88:3822-3828, JUN 2005
abstract, full text

Bathe, M., Rutledge, G.C., Grodzinsky, A.J., Tidor, B.
A coarse-grained molecular model for glycosaminoglycans: Application to chondroitin, chondroitin sulfate, and hyaluronic acid
BIOPHYSICAL JOURNAL, 88:3870-3887, JUN 2005
abstract, full text

Croixmarie, V., Briki, F., David, G., Coic, Y.M., Ovtracht, L., Doucet, J., Jamin, N., Sanson, A.
A cylinder-shaped double ribbon structure formed by an amyloid hairpin peptide derived from the beta-sheet of murine PrP: An X-ray and molecular dynamics simulation study
JOURNAL OF STRUCTURAL BIOLOGY, 150:284-299, JUN 2005
abstract, full text

Ebetino, F.H., Roze, C.N., McKenna, C.E., Barnett, B.L., Dunford, J.E., Russell, R.G.G., Mieling, G.E., Rogers, M.J.
Molecular interactions of nitrogen-containing bisphosphonates within farnesyl diphosphate synthase
JOURNAL OF ORGANOMETALLIC CHEMISTRY, 690:2679-2687, MAY 16 2005
abstract, full text

Liu, S.M., Stewart, M.
Structural basis for the high-affinity binding of nucleoporin Nup1p to the Saccharomyces cerevisiae importin-beta homologue, Kap95p
JOURNAL OF MOLECULAR BIOLOGY, 349:515-525, JUN 10 2005
abstract, full text

Lipfert, J., Franklin, J., Wu, F., Doniach, S.
Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: Simulation by reaction path annealing
JOURNAL OF MOLECULAR BIOLOGY, 349:648-658, JUN 10 2005
abstract, full text

Melquiond, A., Boucher, G., Mousseau, N., Derreumaux, P.
Following the aggregation of amyloid-forming peptides by computer simulations
JOURNAL OF CHEMICAL PHYSICS, 122: Art. No. 174904, MAY 1 2005
abstract, full text

Lahiri, P., Chaudhuri, U., Chattopadhyay, A., Chakraborty, P., Mandal, D., Dasgupta, A.K.
Structural insights in platelet receptor synergism-antiplatelet therapy in post-ischemic cerebrovascular events
BLOOD CELLS MOLECULES AND DISEASES, 34:248-256, MAY-JUN 2005
abstract, full text

Leonov, H., Arkin, I.T.
A periodicity analysis of transmembrane helices
BIOINFORMATICS, 21:2604-2610, JUN 1 2005
abstract, full text

Mazumder-Shivakumar, D., Bruice, T.C.
Computational study of IAG-nucleoside hydrolase: Determination of the preferred ground state conformation and the role of active site residues
BIOCHEMISTRY, 44:7805-7817, MAY 31 2005
abstract, full text

Gong, R., Peng, X.X., Kang, S.L., Feng, H.X., Huang, J.Y., Zhang, W.T., Lin, D.H., Tien, P., Xiao, G.F.
Structural characterization of the fusion core in syncytin, envelope protein of human endogenous retrovirus family W
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 331:1193-1200, JUN 17 2005
abstract, full text

Brigo, A., Lee, K.W., Fogolari, F., Mustata, G.L., Briggs, J.M.
Comparative molecular dynamics simulations of HIV-1 integrase and the T66I/M154I mutant: Binding modes and drug resistance to a diketo acid inhibitor
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 59:723-741, JUN 1 2005
abstract, full text

Etchebest, C., Benros, C., Hazout, S., de Brevern, A.G.
A structural alphabet for local protein structures: Improved prediction methods
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 59:810-827, JUN 1 2005
abstract, full text

Fujisaki, H., Straub, J.E.
Vibrational energy relaxation in proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:6726-6731, MAY 10 2005
abstract, full text

Villa, E., Balaeff, A., Schulten, K.
Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:6783-6788, MAY 10 2005
abstract, full text

Law, R.J., Henchman, R.H., McCammon, J.A.
A gating mechanism proposed from a simulation of a human alpha 7 nicotinic acetylcholine receptor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:6813-6818, MAY 10 2005
abstract, full text

Fischer, S., Windshugel, B., Horak, D., Holmes, K.C., Smith, J.C.
Structural mechanism of the recovery stroke in the myosin molecular motor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:6873-6878, MAY 10 2005
abstract, full text

Lu, G., Maragakis, P., Kaxiras, E.
Carbon nanotube interaction with DNA
NANO LETTERS, 5:897-900, MAY 2005
abstract, full text

Bishop, T.C.
Molecular dynamics simulations of a nucleosome and free DNA
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 22:673-685, JUN 2005
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Rauch, C., Trieb, M., Wibowo, F.R., Wellenzohn, B., Mayer, E., Liedl, K.R.
Towards an understanding of DNA recognition by the methyl-CpG binding domain 1
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 22:695-706, JUN 2005
abstract, full text

Grotjohann, I., Fromme, P.
Structure of cyanobacterial Photosystem I
PHOTOSYNTHESIS RESEARCH, 85:51-72, JUL 2005
abstract, full text

Veselkov, A.N., Djimant, L.N., Veselkov, K.A., Davies, D.B.
Structural analysis of the complex of phenoxazone antibiotic actinocyl-bis(2-dimethylaminoethyl)amide with deoxytetranucleotide 5 '-d(TpGpCpA) by two-dimensional H-1-NMR spectroscopy and molecular mechanics
MOLECULAR BIOLOGY, 39:298-305, MAR-APR 2005
abstract, full text

Konig, P.H., Hoffmann, M., Frauenheim, T., Cui, Q.
A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method
JOURNAL OF PHYSICAL CHEMISTRY B, 109:9082-9095, MAY 12 2005
abstract, full text

Foloppe, N., Nilsson, L.
Toward a full characterization of nucleic acid components in aqueous solution: Simulations of nucleosides
JOURNAL OF PHYSICAL CHEMISTRY B, 109:9119-9131, MAY 12 2005
abstract, full text

Chen, Z.L., Zhao, H.M.
Rapid creation of a novel protein function by in vitro coevolution
JOURNAL OF MOLECULAR BIOLOGY, 348:1273-1282, MAY 20 2005
abstract, full text

Wang, Y.Z., Feng, L., Said, M., Balderman, S., Fayazi, Z., Liu, Y., Ghosh, D., Gulick, A.M.
Analysis of the 2.0 angstrom crystal structure of the protein-DNA complex of the human PDEF ets domain bound to the prostate specific antigen regulatory site
BIOCHEMISTRY, 44:7095-7106, MAY 17 2005
abstract, full text

Bulaj, G., West, P.J., Garrett, J.E., Marsh, M., Zhang, M.M., Norton, R.S., Smith, B.J., Yoshikami, D., Olivera, B.M.
Novel conotoxins from Conus striatus and Conus kinoshitai selectively block TTX-resistant sodium channels
BIOCHEMISTRY, 44:7259-7265, MAY 17 2005
abstract, full text

Barrett, C.P., Noble, M.E.M.
Molecular motions of human cyclin-dependent kinase 2
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:13993-14005, APR 8 2005
abstract, full text

Lee, J.E., Singh, V., Evans, G.B., Tyler, P.C., Furneaux, R.H., Cornell, K.A., Riscoe, M.K., Schramm, V.L., Howell, P.L.
Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5 '-methylthioadenosine/S-adenosylhomocysteine nucleosidase
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:18274-18282, MAY 6 2005
abstract, full text

Pelmenschikov, V., Siegbahn, P.E.M.
Copper-zinc superoxide dismutase: Theoretical insights into the catalytic mechanism
INORGANIC CHEMISTRY, 44:3311-3320, MAY 2 2005
abstract, full text

Proks, P., Girard, C., Haider, S., Gloyn, A.L., Hattersley, A.T., Sansom, M.S.P., Ashcroft, F.M.
A gating mutation at the internal mouth of the Kir6.2 pore is associated with DEND syndrome
EMBO REPORTS, 6:470-475, MAY 2005
abstract, full text

Dlugosz, M., Bzowska, A., Antosiewicz, J.M.
Stopped-flow studies of guanine binding by calf spleen purine nucleoside phosphorylase
BIOPHYSICAL CHEMISTRY, 115:67-76, MAY 1 2005
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Zhang, Q.M., Jaroniec, J., Lee, G., Marszalek, P.E.
Direct detection of inter-residue hydrogen bonds in polysaccharides by single-molecule force spectroscopy
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 44:2723-2727, 2005
full text

Sotomayor, M