NAMD Papers and Citations
A list of papers citing NAMD is included below.
How to Cite NAMD
The NAMD License Agreement specifies that any reports or published results obtained with NAMD shall acknowledge its use and credit the developers as:
"NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign."
Any published work which utilizes NAMD shall include the following reference:
James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005. abstract, journal
Electronic documents shall include a direct link to the official NAMD page:
Proper citation is essential to continued NIH funding for NAMD development, as it is a primary way in which we demonstrate the value of our software to the scientific community. Thank you for your attention to these details.
Papers About NAMD
Sameer Kumar, Chao Huang, Gengbin Zheng, Eric Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, and Laxmikant V. Kale. Scalable Molecular Dynamics with NAMD on Blue Gene/L. Submitted to IBM Journal of Research and Development. 2007. abstract
K.Y. Sanbonmatsu and C.-S. Tung. High performance computing in biology: Multimillion atom simulations of nanoscale systems. Journal of Structural Biology, 157:470-480, 2007. journal
Michelle Gower, Jordi Cohen, James Phillips, Richard Kufrin, and Klaus Schulten. Managing biomolecular simulations in a grid environment with NAMD-G. Proceedings of the 2006 TeraGrid Conference, 2006. In Press. abstract
Sameer Kumar, Chao Huang, Gheorghe Almasi, and Laxmikant V. Kale. Achieving Strong Scaling with NAMD on Blue Gene/L. Proceedings of IEEE International Parallel & Distributed Processing Symposium 2006, 2006. abstract
Laxmikant V. Kale, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng. Biomolecular modeling using parallel supercomputers. In S. Aluru, editor, Handbook of computational molecular biology, pp. 34.1-34.43. Taylor and Francis, 2005. abstract
James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005. abstract, journal
Joachim Hein, Fiona Reid, Lorna Smith, Ian Bush, Martyn Guest, and Paul Sherwood. On the performance of molecular dynamics applications on current high-end systems. Phil. Trans. R. Soc. A, 363:1987-1998, 2005. journal
James C. Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant V. Kalé. NAMD: Biomolecular Simulation on Thousands of Processors. Proceedings of the IEEE/ACM SC2002 Conference. IEEE Press, 2002. Technical Paper 277. abstract, pdf
Robert K. Brunner, James C. Phillips, Laxmikant V. Kalé. Scalable Molecular Dynamics for Large Biomolecular Systems. Proceedings of the IEEE/ACM SC2000 Conference. IEEE Press, 2000. Technical Paper 271. abstract, pdf
R. Sharma, M. Zeller, V. I. Pavlovic, T. S. Huang, Z. Lo, S. Chu, Y. Zhao, J. Phillips, and K. Schulten. Speech/Gesture Interface to a Visual Computing Environment. IEEE Computer Graphics and Applications, March/April 2000, 29-37. abstract,
Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151:283-312, 1999. abstract
Robert Brunner, Laxmikant Kalé, and James Phillips. Flexibility and Inter-operability in a Parallel Biomolecular Dynamics Code. In M.E. Henderson, C.R. Anderson, and S.L. Lyons, editors, Object Oriented Methods for Interoperable Scientific and Engineering Computing, Proceedings in Applied Mathematics 99, 1999.
James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten. Avoiding algorithmic obfuscation in a message-driven parallel MD code. In P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Engineering, 4:472-482, 1999. Springer-Verlag. abstract
L. V. Kalé, M. Bhandarkar, R. Brunner, N. Krawetz, J. Phillips, and A. Shinozaki. NAMD: A Case Study in Multilingual Parallel Programming. In Z. Li, P.-C. Yew, S. Chatterjee, C.-H. Huang, P. Sadayappan, and D. Sehr, editors, Languages and Compilers for Parallel Computing, Lecture Notes in Computer Science, 1366:367-381, 1998. Springer-Verlag. abstract, postscript
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten. NAMD---A parallel, object-oriented molecular dynamics program. International Journal of Supercomputer Applications and High Performance Computing, 10:251-268, 1996. abstract
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert Skeel, Klaus Schulten, and Richard Kufrin. MDScope---A visual computing environment for structural biology. Computational Physics Communications, 91:111-134, 1995. abstract
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert Skeel, Klaus Schulten, and Richard Kufrin. MDScope---A visual computing environment for structural biology. In S.N. Atluri, G. Yagawa, and T.A. Cruse, editors, Computational Mechanics 95, volume 1, pages 476-481, 1995. abstract
Papers Citing NAMD
The "full text" links lead to Google Scholar searches for the article. We do not provide copies of these articles ourselves. Articles by TCBG members are available in the TCBG Publications Database.
List generated July 19, 2006.
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
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Starovoitova, V., Budarz, T.E., Wyllie, G.R.A., Scheidt, W.R., Sturhahn, W., Alp, E.E., Prohofsky, E.W., Durbin, S.M.
Vibrational spectroscopy and normal-mode analysis of Fe(II) octaethylporphyrin
JOURNAL OF PHYSICAL CHEMISTRY B, 110:13277-13282, JUL 6 2006
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Krautler, V., Hunenberger, P.H.
A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 27:1163-1176, AUG 2006
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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
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Gracheva, M.E., Aksimentiev, A., Leburton, J.P.
Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor
NANOTECHNOLOGY, 17:3160-3165, JUL 14 2006
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Mezei, M., Filizola, M.
TRAJELIX: A computational tool for the geometric characterization of protein helices during molecular dynamics simulations
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 20:97-107, FEB 2006
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Paliwal, A., Asthagiri, D., Pratt, L.R., Ashbaugh, H.S., Paulaitis, M.E.
An analysis of molecular packing and chemical association in liquid water using quasichemical theory
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 224502, JUN 14 2006
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Moskovsky, A.A., Vanovschi, V.V., Konyukhov, S.S., Nemukhin, A.V.
Implementation of the replica-exchange molecular dynamics method for rigid bodies
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 106:2208-2213, AUG 15 2006
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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
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Bastug, T., Kuyucak, S.
Molecular dynamics simulations of calcium binding in gramicidin A
CHEMICAL PHYSICS LETTERS, 424:82-85, JUN 12 2006
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Lyman, E., Zuckerman, D.M.
Ensemble-based convergence analysis of biomolecular trajectories
BIOPHYSICAL JOURNAL, 91:164-172, JUL 2006
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Pedretti, A., Vistoli, G., Marconi, C., Testa, B.
Muscarinic receptors: A comparative analysis of structural features and binding modes through homology modelling and molecular docking
CHEMISTRY & BIODIVERSITY, 3:481-501, 2006
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Interlandi, G., Settanni, G., Caflisch, A.
Unfolding transition state and intermediates of the tumor suppressor p16(INK4a) investigated by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 64:178-192, JUL 1 2006
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Karain, W.I., Qaraeen, N.I., Ajarmah, B.
A stochastic model for correlated protein motions
PHYSICS LETTERS A, 354:497-500, JUN 12 2006
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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
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Jacobsen, R.B., Sale, K.L., Ayson, M.J., Novak, P., Hong, J.H., Lane, P., Wood, N.L., Kruppa, G.H., Young, M.M., Schoeniger, J.S.
Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry
PROTEIN SCIENCE, 15:1303-1317, JUN 2006
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Pedretti, A., Villa, M., Pallavicini, M., Valoti, E., Vistoli, G.
Construction of human ghrelin receptor (hGHS-R1a) model using a fragmental prediction approach and validation through docking analysis
JOURNAL OF MEDICINAL CHEMISTRY, 49:3077-3085, JUN 1 2006
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Vistoli, G., Pedretti, A., Cattaneo, M., Aldini, G., Testa, B.
Homology modeling of human serum carnosinase, a potential medicinal target, and MD simulations of its allosteric activation by citrate
JOURNAL OF MEDICINAL CHEMISTRY, 49:3269-3277, JUN 1 2006
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Gu, Y., VanCourt, T., Herbordt, M.C.
Accelerating molecular dynamics simulations with configurable circuits
IEE PROCEEDINGS-COMPUTERS AND DIGITAL TECHNIQUES, 153:189-195, MAY 2006
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Patny, A., Desai, P.V., Avery, M.A.
Homology modeling of G-protein-coupled receptors and implications in drug design
CURRENT MEDICINAL CHEMISTRY, 13:1667-1691, 2006
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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
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Zanuy, D., Casanovas, J., Aleman, C.
Conformational features of an actuator containing calix[4] arene and thiophene: A molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 110:9876-9881, MAY 25 2006
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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
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Manetti, F., Tintori, C., Armand-Ugon, M., Clotet-Codina, I., Massa, S., Ragno, R., Este, J.A., Botta, M.
A combination of molecular dynamics and docking calculations to explore the binding mode of ADS-J1, a polyanionic compound endowed with anti-HIV-1 activity
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46:1344-1351, MAY 2006
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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
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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
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Plummer, M., Hein, J., Guest, M.F., D'Mellow, K.J., Bush, I.J., Refson, K., Pringle, G.J., Smith, L., Trew, A.
Terascale materials modelling on high performance system HPCx
JOURNAL OF MATERIALS CHEMISTRY, 16:1885-1893, 2006
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Bowers, K.J., Dror, R.O., Shaw, D.E.
The midpoint method for parallelization of particle simulations
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 184109, MAY 14 2006
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Lopez, C.F., Nielsen, S.O., Srinivas, G., DeGrado, W.F., Klein, M.L.
Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:649-655, MAY 2006
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Rodinger, T., Howell, P.L., Pomes, R.
Distributed replica sampling
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:725-731, MAY 2006
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Adcock, S.A., McCammon, J.A.
Molecular dynamics: Survey of methods for simulating the activity of proteins
CHEMICAL REVIEWS, 106:1589-1615, MAY 2006
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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
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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
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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
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Dixon, M.F.
A runtime adaptive load balancing algorithm for particle simulations
APPLIED PARALLEL COMPUTING: STATE OF THE ART IN SCIENTIFIC COMPUTING, 3732:709-718, 2006
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Pickholz, M., Oliveira, O.N., Skaf, M.S.
Molecular dynamics simulations of neutral chlorpromazine in zwitterionic phospholipid monolayers
JOURNAL OF PHYSICAL CHEMISTRY B, 110:8804-8814, MAY 4 2006
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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
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Eike, D.M., Maginn, E.J.
Atomistic simulation of solid-liquid coexistence for molecular systems: Application to triazole and benzene
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 164503, APR 28 2006
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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
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Limbach, H.J., Arnold, A., Mann, B.A., Holm, C.
ESPResSo - an extensible simulation package for research on soft matter systems
COMPUTER PHYSICS COMMUNICATIONS, 174:704-727, MAY 1 2006
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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
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Lagerqvist, J., Zwolak, M., Di Ventra, M.
Fast DNA sequencing via transverse electronic transport
NANO LETTERS, 6:779-782, APR 2006
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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
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Xu, L.N., Zhang, L.L., Gu, Z., Zhou, L.X.
Full electronic structure calculation of the biological activity in P173L enzyme
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 106:1544-1550, JUN 2006
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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
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Balaeff, A., Mahadevan, L., Schulten, K.
Modeling DNA loops using the theory of elasticity
PHYSICAL REVIEW E, 73: Art. No. 031919, MAR 2006
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Chipot, C., Tarek, M.
Interaction of a peptide nanotube with a water-membrane interface
PHYSICAL BIOLOGY, 3:S20-S25, MAR 2006
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Lu, D.Y., Aksimentiev, A., Shih, A.Y., Cruz-Chu, E., Freddolino, P.L., Arkhipov, A., Schulten, K.
The role of molecular modeling in bionanotechnology
PHYSICAL BIOLOGY, 3:S40-S53, MAR 2006
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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
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Hwang, H., Schatz, G.C., Ratner, M.A.
Ion current calculations based on three dimensional Poisson-Nernst-Planck theory for a cyclic peptide nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 110:6999-7008, APR 6 2006
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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
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Zhao, X.G., Cummings, P.T.
Molecular dynamics study of carbon nanotube oscillators revisited
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 134705, APR 7 2006
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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
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Gao, M., Schulten, K.
Onset of anthrax toxin pore formation
BIOPHYSICAL JOURNAL, 90:3267-3279, MAY 2006
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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
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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
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Maciejczyk, M., Hermans, J., Bierzynski, A.
Free energy of helix propagation in short polyalanine chains determined from peptide growth simulations of La3+-binding model peptides. Comparison with experimental data
ACTA BIOCHIMICA POLONICA, 53:121-129, 2006
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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
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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
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Cecchini, M., Curcio, R., Pappalardo, M., Melki, R., Caflisch, A.
A molecular dynamics approach to the structural characterization of amyloid aggregation
JOURNAL OF MOLECULAR BIOLOGY, 357:1306-1321, APR 7 2006
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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
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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
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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
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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
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Fitch, C.A., Whitten, S.T., Hilser, V.J., Garcia-Moreno, B.
Molecular mechanisms of pH-driven conformational transitions of proteins: Insights from continuum electrostatics calculations of acid unfolding
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 63:113-126, APR 1 2006
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Meyer, T., Ferrer-Costa, C., Perez, A., Rueda, M., Bidon-Chanal, A., Luque, F.J., Laughton, C.A., Orozco, M.
Essential dynamics: A tool for efficient trajectory compression and management
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:251-258, MAR-APR 2006
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Pophristic, V., Vemparala, S., Ivanov, I., Liu, Z.W., Klein, M.L., DeGrado, W.F.
Controlling the shape and flexibility of arylamides: A combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3517-3526, MAR 2 2006
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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
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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
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Yan, L.M., Ma, Y.F., Seminario, J.M.
Encoding information using molecular vibronics
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 6:675-684, MAR 2006
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Jensen, M.O., Mouritsen, O.G.
Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF
BIOPHYSICAL JOURNAL, 90:2270-2284, APR 2006
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Bastug, T., Gray-Weale, A., Patra, S.M., Kuyucak, S.
Role of protein flexibility in ion permeation: A case study in gramicidin A
BIOPHYSICAL JOURNAL, 90:2285-2296, APR 2006
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Gumbart, J., Schulten, K.
Molecular dynamics studies of the archaeal translocon
BIOPHYSICAL JOURNAL, 90:2356-2367, APR 2006
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Anishkin, A., Sukharev, S., Colombini, M.
Searching for the molecular arrangement of transmembrane ceramide channels
BIOPHYSICAL JOURNAL, 90:2414-2426, APR 2006
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Zhu, Y.M., Smith, D., Verma, C., Lim, W.G., Tan, B.J., Armstrong, J.S., Zhou, S.F., Chan, E., Tan, S.L., Zhu, Y.Z., Cheung, N.S., Duan, W.
The very C-terminus of protein kinase C epsilon is critical for the full catalytic competence but its hydrophobic motif is dispensable for the interaction with 3-phosphoinositide-dependent kinase-1
CELLULAR SIGNALLING, 18:807-818, JUN 2006
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Gracheva, M.E., Xiong, A.L., Aksimentiev, A., Schulten, K., Timp, G., Leburton, J.P.
Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor
NANOTECHNOLOGY, 17:622-633, FEB 14 2006
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Zhuang, W., Abramavicius, D., Hayashi, T., Mukamel, S.
Simulation protocols for coherent femtosecond vibrational spectra of peptides
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3362-3374, FEB 23 2006
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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
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Chipot, C., Rozanska, X., Dixit, S.B.
Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 19:765-770, NOV 2005
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Ivanov, I., Vemparala, S., Pophristic, V., Kuroda, K., DeGrado, W.F., McCammon, J.A., Klein, M.L.
Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:1778-1779, FEB 15 2006
full text
Cadena, C., Zhao, Q., Snurr, R.Q., Maginn, E.J.
Molecular modeling and experimental studies of the thermodynamic and transport properties of pyridinium-based ionic liquids
JOURNAL OF PHYSICAL CHEMISTRY B, 110:2821-2832, FEB 16 2006
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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
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Casanovas, J., Zanuy, D., Aleman, C.
Conducting polymer actuator mechanism based on the conformational flexibility of calix[4]arene
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 45:1103-1105, 2006
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Seroka, P., Plosinski, M., Czub, J., Sowinski, P., Pawlak, J.
Monosaccharides as internal probes for the determination of the absolute configuration of 2-butanol
MAGNETIC RESONANCE IN CHEMISTRY, 44:132-138, FEB 2006
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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
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Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
The existence of a second allosteric site on the M-1 muscarinic acetylcholine receptor and its implications for drug design
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 16:1217-1220, MAR 1 2006
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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
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Wells, S., Menor, S., Hespenheide, B., Thorpe, M.F.
Constrained geometric simulation of diffusive motion in proteins
PHYSICAL BIOLOGY, 2:S127-S136, DEC 2005
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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
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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
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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
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Gullingsrud, J., Kim, C., Taylor, S.S., McCammon, J.A.
Dynamic binding of PKA regulatory subunit RI alpha
STRUCTURE, 14:141-149, JAN 2006
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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
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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
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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
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Park, S., Saven, J.G.
Simulation of pH-dependent edge strand rearrangement in human beta-2 microglobulin
PROTEIN SCIENCE, 15:200-207, JAN 2006
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Martinez, L., Webb, P., Polikarpov, I., Skaf, M.S.
Molecular dynamics simulations of ligand dissociation from thyroid hormone receptors: Evidence of the likeliest escape pathway and its implications for the design of novel ligands
JOURNAL OF MEDICINAL CHEMISTRY, 49:23-26, JAN 12 2006
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Kale, L.V., Zheng, G.B., Lee, C.W., Kumar, S.
Scaling applications to massively parallel machines using Projections performance analysis tool
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING THEORY METHODS AND APPLICATIONS, 22:347-358, FEB 2006
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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
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Heng, J.B., Aksimentiev, A., Ho, C., Marks, P., Grinkova, Y.V., Sligar, S., Schulten, K., Timp, G.
The electromechanics of DNA in a synthetic nanopore
BIOPHYSICAL JOURNAL, 90:1098-1106, FEB 2006
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Azevedo, P.J., Silva, C.G., Rodrigues, J.R., Loureiro-Ferreira, N., Brito, R.M.M.
Detection of hydrophobic clusters in molecular dynamics protein unfolding simulations using association rules
BIOLOGICAL AND MEDICAL DATA ANALYSIS, PROCEEDINGS, 3745:329-337, 2005
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Lim, R.Y.H., Aebi, U.
In silico access to the nuclear pore complex
STRUCTURE, 13:1741-1743, DEC 2005
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Isgro, T.A., Schulten, K.
Binding dynamics of isolated nucleoporin repeat regions to importin-beta
STRUCTURE, 13:1869-1879, DEC 2005
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Wang, P., Yan, B., Guo, J.T., Hicks, C., Xu, Y.
Structural genomics analysis of alternative splicing and application to isoform structure modeling
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:18920-18925, DEC 27 2005
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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
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Senapati, S., Bui, J.M., McCammon, J.A.
Induced fit in mouse acetylcholinesterase upon binding a femtomolar inhibitor: A molecular dynamics study
JOURNAL OF MEDICINAL CHEMISTRY, 48:8155-8162, DEC 29 2005
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Chipot, C., Henin, J.
Exploring the free-energy landscape of a short peptide using an average force
JOURNAL OF CHEMICAL PHYSICS, 123: Art. No. 244906, DEC 22 2005
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Coveney, P.V., Fowler, P.W.
Modelling biological complexity: a physical scientist's perspective
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 2:267-280, SEP 22 2005
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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
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Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
Identification of multiple allosteric sites on the M-1 muscarinic acetylcholine receptor
FEBS LETTERS, 579:6726-6732, DEC 19 2005
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Sohn, R., Parks, J.A., Buhrman, G., Brown, P., Kristjansdottir, K., Safi, A., Edelsbrunner, H., Yang, W.T., Rudolph, J.
Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate
BIOCHEMISTRY, 44:16563-16573, DEC 20 2005
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Chung, S.H., Corry, B.
Three computational methods for studying permeation, selectivity and dynamics in biological ion channels
SOFT MATTER, 1:417-427, DEC 14 2005
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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
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Likic, V.A., Gooley, P.R., Speed, T.P., Strehler, E.E.
A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics
PROTEIN SCIENCE, 14:2955-2963, DEC 2005
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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
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Wan, S.Z., Coveney, P.V., Flower, D.R.
Molecular basis of peptide recognition by the TCR: Affinity differences calculated using large scale computing
JOURNAL OF IMMUNOLOGY, 175:1715-1723, AUG 1 2005
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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
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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
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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
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Thomas, S., Tanase, G., Dale, L.K., Moreira, J.M., Rauchwerger, L., Amato, N.M.
Parallel protein folding with STAPL
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 17:1643-1656, DEC 10 2005
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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
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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
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Baudry, J., Smith, J.C.
Can proteins and crystals self-catalyze methyl rotations?
JOURNAL OF PHYSICAL CHEMISTRY B, 109:20572-20578, NOV 3 2005
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Seminario, J.M., Yan, L.M., Ma, Y.F.
Transmission of vibronic signals in molecular circuits
JOURNAL OF PHYSICAL CHEMISTRY A, 109:9712-9715, NOV 3 2005
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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
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Vistoli, G., Pedretti, A., Villa, L., Testa, B.
Solvent constraints on the property space of acetylcholine. 2. Ordered media
JOURNAL OF MEDICINAL CHEMISTRY, 48:6926-6935, NOV 3 2005
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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
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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
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Gorfe, A.A., Caflisch, A.
Functional plasticity in the substrate binding site of beta-secretase
STRUCTURE, 13:1487-1498, OCT 2005
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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
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Wang, W., Skeel, R.D.
Fast evaluation of polarizable forces
JOURNAL OF CHEMICAL PHYSICS, 123: Art. No. 164107, OCT 22 2005
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Choi, S., Clements, D.J., Pophristic, V., Ivanov, I., Vemparala, S., Bennett, J.S., Klein, M.L., Winkler, J.D., DeGrado, W.E.
The design and evaluation of heparin-binding foldamers
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 44:6685-6689, 2005
full text
Filipek, S.
Organization of rhodopsin molecules in native membranes of rod cells - an old theoretical model compared to new experimental data
JOURNAL OF MOLECULAR MODELING, 11:385-391, SEP 2005
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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
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Rai, B.K., Prohofsky, E.W., Durbin, S.M.
Single-atom test of all-atom empirical potentials: Fe in myoglobin
JOURNAL OF PHYSICAL CHEMISTRY B, 109:18983-18987, OCT 13 2005
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full text
Jha, S., Coveney, P.V., Laughton, C.A.
Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1617-1627, NOV 30 2005
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De Luca, L., Vistoli, G., Pedretti, A., Barreca, M.L., Chimirri, A.
Molecular dynamics studies of the full-length integrase-DNA complex
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 336:1010-1016, NOV 4 2005
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Li, A.Q., Dowell, E.H.
Modal reduction of mathematical models of biological molecules
JOURNAL OF COMPUTATIONAL PHYSICS, 211:262-288, JAN 1 2006
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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
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Seminario, J.M., Yan, L.M., Ma, Y.F.
Scenarios for molecular-level signal processing
PROCEEDINGS OF THE IEEE, 93:1753-1764, OCT 2005
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Franklin, J., Doniach, S.
Adaptive time stepping in biomolecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 123: Art. No. 124909, SEP 22 2005
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Yonkunas, M.J., Xu, Y., Tang, P.
Anesthetic interaction with ketosteroid isomerase: Insights from molecular dynamics simulations
BIOPHYSICAL JOURNAL, 89:2350-2356, OCT 2005
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Pedersen, T.B., Kaasgaard, T., Jensen, M.O., Frokjaer, S., Mouritsen, O.G., Jorgensen, K.
Phase behavior and nanoscale structure of phospholipid membranes incorporated with acylated C-14-peptides
BIOPHYSICAL JOURNAL, 89:2494-2503, OCT 2005
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Stagg, S.M., Harvey, S.C.
Exploring the flexibility of ribosome recycling factor using molecular dynamics
BIOPHYSICAL JOURNAL, 89:2659-2666, OCT 2005
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Kamath, S.A., Buolamwini, J.K.
Asp746 to glycine change may have a greater influence than cys751 to serine change in accounting for ligand selectivity between EGFR and HER-2 at the ATP site
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 19:287-291, MAY 2005
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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
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Witheesuk, E.J., Samudrala, R.
Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach
ANTIVIRAL THERAPY, 10:157-166, 2005
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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
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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
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Pickles, S.M., Haines, R., Pinning, R.L., Porter, A.R.
A practical toolkit for computational steering
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1843-1853, AUG 15 2005
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Kalawsky, R.S., Nee, S.P., Holmes, I., Coveney, P.V.
A grid-enabled lightweight computational steering client: a .NET PDA implementation
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1885-1894, AUG 15 2005
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Hein, J.I., Reid, F., Smith, L., Bush, I., Guest, M., Sherwood, P.
On the performance of molecular dynamics applications on current high-end systems
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1987-1998, AUG 15 2005
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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
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full text
Woods, C.J., Ng, M.H., Johnston, S., Murdock, S.E., Wu, B., Tai, K., Fangohr, H., Jeffreys, P., Cox, S., Frey, J.G., Sansom, M.S.P., Essex, J.W.
Grid computing and biomolecular simulation
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2017-2035, AUG 15 2005
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Wan, S.Z., Coveney, P.V., Flower, D.R.
Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2037-2053, AUG 15 2005
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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
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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
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full text
Wiley, A.P., Swain, M.T., Phillips, S.C., Essex, J.W., Edge, C.M.
Parametrization of reversible digitally filtered molecular dynamics simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 1:24-35, JAN-FEB 2005
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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
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Bae, E., Phillips, G.N.
Identifying and engineering ion pairs in adenylate kinases
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:30943-30948, SEP 2 2005
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Paliwal, A., Asthagiri, D., Abras, D., Lenhoff, A.M., Paulaitis, M.E.
Light-scattering studies of protein solutions: Role of hydration in weak protein-protein interactions
BIOPHYSICAL JOURNAL, 89:1564-1573, SEP 2005
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full text
Makrodimitris, K., Fernandez, E.J., Woolf, T.B., O'Connell, J.P.
ALLD: An object-oriented mesoscopic simulation program for polar biomolecules in hydrophobic chromatography or biomembranes
MOLECULAR SIMULATION, 31:623-636, AUG 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
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full text
Dublet, B., Ruello, A., Pederzoli, M., Hajjar, E., Courbebaisse, M., Canteloup, S., Reuter, N., Witko-Sarsat, V.
Cleavage of p21/WAF1/CIP1 by proteinase 3 modulates differentiation of a monocytic cell line
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:30242-30253, AUG 26 2005
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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
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Mulkidjanian, A.Y., Kozlova, M.A., Cherepanov, D.A.
Ubiquinone reduction in the photosynthetic reaction centre of Rhodobacter sphaeroides: interplay between electron transfer, proton binding and flips of the quinone ring
BIOCHEMICAL SOCIETY TRANSACTIONS, 33:845-850, AUG 2005
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Debnath, A.K.
Application of 3D-QSAR techniques in anti-HIV-1 drug design - An overview
CURRENT PHARMACEUTICAL DESIGN, 11:3091-3110, 2005
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de Brevern, A.G., Wong, H., Tournamille, C., Colin, Y., Van Kim, C.L., Etchebest, C.
A structural model of a seven-transmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC)
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1724:288-306, AUG 5 2005
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Ota, N., Agard, D.A.
Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
JOURNAL OF MOLECULAR BIOLOGY, 351:345-354, AUG 12 2005
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Aldini, G., Dalle-Donne, I., Vistoli, G., Facino, R.M., Carini, M.
Covalent modification of actin by 4-hydroxy-trans-2-nonenal (HNE): LC-ESI-MS/MS evidence for Cys374 Michael adduction
JOURNAL OF MASS SPECTROMETRY, 40:946-954, JUL 2005
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full text
Ashworth, M., Bush, I.J., Guest, M.F., Sunderland, A.G., Booth, S., Hein, J., Smith, L., Stratford, K., Curioni, A.
HPCx: towards capability computing
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 17:1329-1361, AUG 25 2005
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full text
McGillivray, G., Savarirayan, R., Cox, T.C., Stojkoski, C., McNeil, R., Bankier, A., Bateman, J.F., Roscioli, T., Gardner, R.J.M., Lamande, S.R.
Familial scaphocephaly syndrome caused by a novel mutation in the FGFR2 tyrosine kinase domain
JOURNAL OF MEDICAL GENETICS, 42:656-662, AUG 2005
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Carrillo-Tripp, M., Feller, S.E.
Evidence for a mechanism by which omega-3 polyunsaturated lipids may affect membrane protein function
BIOCHEMISTRY, 44:10164-10169, AUG 2 2005
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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
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full text
Park, S., Saven, J.G.
Statistical and molecular dynamics studies of buried waters in globular proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 60:450-463, AUG 15 2005
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full text
Lynch, D.L., Reggio, P.H.
Molecular dynamics simulations of the endocannabinoid N-arachidonoylethanolamine (Anandamide) in a phospholipid bilayer: Probing structure and dynamics
JOURNAL OF MEDICINAL CHEMISTRY, 48:4824-4833, JUL 28 2005
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Roh, J.H., Novikov, V.N., Gregory, R.B., Curtis, J.E., Chowdhuri, Z., Sokolov, A.P.
Onsets of anharmonicity in protein dynamics
PHYSICAL REVIEW LETTERS, 95: Art. No. 038101, JUL 15 2005
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Borza, D.B., Bondar, O., Colon, S., Todd, P., Sado, Y., Neilson, E.G., Hudson, B.G.
Goodpasture autoantibodies unmask cryptic epitopes by selectively dissociating autoantigen complexes lacking structural reinforcement - Novel mechanisms for immune privilege and autoimmune pathogenesis
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:27147-27154, JUL 22 2005
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Zheng, G.B., Wilmarth, T., Jagadishprasad, P., Kale, L.V.
Simulation-based performance prediction for large parallel machines
INTERNATIONAL JOURNAL OF PARALLEL PROGRAMMING, 33:183-207, JUN 2005
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Damjanovic, A., Garcia-Moreno, B., Lattman, E.E., Garcia, A.E.
Molecular dynamics study of hydration of the protein interior
COMPUTER PHYSICS COMMUNICATIONS, 169:126-129, JUL 1 2005
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Maggs, A.C., Rottler, J.
Auxiliary field simulation and Coulomb's law
COMPUTER PHYSICS COMMUNICATIONS, 169:160-165, JUL 1 2005
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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
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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
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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
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Scott, L.R., Clark, T., Bagheri, B.
Education and research challenges in parallel computing
COMPUTATIONAL SCIENCE - ICCS 2005, PT 2, 3515:44-51, 2005
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Fleming, P.J., Rose, G.D.
Do all backbone polar groups in proteins form hydrogen bonds?
PROTEIN SCIENCE, 14:1911-1917, JUL 2005
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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
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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
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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
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Weinbach, Y., Elber, R.
Revisiting and parallelizing SHAKE
JOURNAL OF COMPUTATIONAL PHYSICS, 209:193-206, OCT 10 2005
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Chao, S.D., Kress, J.D., Redondo, A.
Coarse-grained rigid blob model for soft matter simulations
JOURNAL OF CHEMICAL PHYSICS, 122: Art. No. 234912, JUN 15 2005
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Veluraja, K., Margulis, C.J.
Conformational dynamics of sialyl Lewis(x) in aqueous solution and its interaction with selectinE. A study by molecular dynamics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 23:101-111, AUG 2005
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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
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Guo, Y.Y., Blocker, F., Xiao, F., Guo, P.X.
Construction and 3-D computer modeling of connector arrays with tetragonal to decagonal transition induced by pRNA of phi29 DNA-packaging motor
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 5:856-863, JUN 2005
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Zhang, Q.M., Lee, G.R., Marszalek, P.E.
Atomic cranks and levers control sugar ring conformations
JOURNAL OF PHYSICS-CONDENSED MATTER, 17:S1427-S1442, MAY 11 2005
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Marzouk, Y.M., Ghoniem, A.F.
K-means clustering for optimal partitioning and dynamic load balancing of parallel hierarchical N-body simulations
JOURNAL OF COMPUTATIONAL PHYSICS, 207:493-528, AUG 10 2005
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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
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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
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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
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Tarek, M.
Membrane electroporation: A molecular dynamics simulation
BIOPHYSICAL JOURNAL, 88:4045-4053, JUN 2005
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Ortiz, V., Nielsen, S.O., Klein, M.L., Discher, D.E.
Unfolding a linker between helical repeats
JOURNAL OF MOLECULAR BIOLOGY, 349:638-647, JUN 10 2005
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Engle, R.D., Skeel, R.D., Drees, M.
Monitoring energy drift with shadow Hamiltonians
JOURNAL OF COMPUTATIONAL PHYSICS, 206:432-452, JUL 1 2005
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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
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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
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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
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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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Germain, R.S., Zhestkov, Y., Eleftheriou, M., Rayshubskiy, A., Suits, F., Ward, T.J.C., Fitch, B.G.
Early performance data on the Blue Matter molecular simulation framework
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 49:447-455, MAR-MAY 2005
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Costantino, G., Entrena-Guadix, A., Macchiarulo, A., Gioiello, A., Pellicciari, R.
Molecular dynamics simulation of the ligand binding domain of farnesoid X receptor. Insights into helix-12 stability and coactivator peptide stabilization in response to agonist binding
JOURNAL OF MEDICINAL CHEMISTRY