|
| 681. Electrically tunable quenching of DNA fluctuations in biased
solid-state nanopores.
Hu Qiu, Anuj Girdhar, Klaus Schulten, and Jean-Pierre Leburton.
ACS Nano, 10:4482-4488, 2016.
|
| 675. Molecular mechanism of processive 3' to 5' RNA translocation in the
active subunit of the RNA exosome complex.
Lela Vukovic, Christophe Chipot, Debora L. Makino, Elena Conti, and Klaus
Schulten.
Journal of the American Chemical Society, 138:4069-4078, 2016.
|
| 671. Intrinsic stepwise translocation of stretched ssDNA in graphene
nanopores.
Hu Qiu, Aditya Sarathy, Jean-Pierre Leburton, and Klaus Schulten.
Nano Letters, 15:8322-8330, 2015.
|
| 662. Dynamic profiling of double-stranded RNA binding proteins.
Xinlei Wang, Lela Vukovic, Hye Ran Koh, Klaus Schulten, and Sua Myong.
Nucleic Acids Res., 43:7566-7576, 2015.
|
| 658. Comparative dynamics and sequence dependence of DNA and RNA
binding to single walled carbon nanotubes.
Markita P. Landry, Lela Vukovic, Sebastian Kruss, Gili Bisker, Alexandra M.
Landry, Shahrin Islam, Rishabh Jain, Klaus Schulten, and Michael S. Strano.
Journal of Physical Chemistry C, 119:10048-10058, 2015.
|
| 655. Tunable graphene quantum point contact transistor for DNA detection
and characterization.
Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton.
Nanotechnology, 26:134005, 2015.
(10 pages).
|
| 654. Mechanism of substrate translocation by a ring-shaped ATPase motor
at millisecond resolution.
Wen Ma and Klaus Schulten.
Journal of the American Chemical Society, 137:3031-3040, 2015.
|
| 637. Gate-modulated graphene quantum point contact device for DNA
sensing.
Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton.
Journal of Computational Electronics, 13:839-846, 2014.
|
| 632. Substrate recognition and specificity of double-stranded RNA
binding proteins.
Lela Vukovic, Hye Ran Koh, Sua Myong, and Klaus Schulten.
Biochemistry, 53:3457-3466, 2014.
|
| 616. Graphene quantum point contact transistor for DNA sensing.
Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton.
Proceedings of the National Academy of Sciences, USA,
110:16748-16753, 2013.
|
| 606. Detection and quantification of methylation in DNA using
solid-state nanopores.
Jiwook Shim, Gwendolyn I. Humphreys, Bala Murali Venkatesan, Jan Marie Munz,
Xueqing Zou, Chaitanya Sathe, Klaus Schulten, Farhad Kosari, Ann M. Nardulli,
George Vasmatzis, and Rashid Bashir.
Scientific Reports, 3:1389, 2013.
(8 pages).
|
| 605. Mechanism of tetracycline resistance by ribosomal protection protein
Tet(O).
Wen Li, Gemma C. Atkinson, Nehal S. Thakor, Ülar Allas, Chuao-chao Lu,
Kwok-Yan Chan, Tanel Tenson, Klaus Schulten, Kevin S. Wilson, Vasili
Hauryliuk, and Joachim Frank.
4:1477, 2013.
(8 pages).
|
| 603. Fusion pore formation and expansion induced by Ca2+ and
synaptotagmin 1.
Ying Lai, Jiajie Diao, Yanxin Liu, Yuji Ishitsuka, Zengliu Su, Klaus Schulten,
Taekjip Ha, and Yeon-Kyun Shin.
Proceedings of the National Academy of Sciences, USA,
110:1333-1338, 2013.
|
| 602. DNA target sequence identification mechanism for dimer-active
protein complexes.
Markita P. Landry, Xueqing Zou, Lei Wang, Wai Mun Huang, Klaus Schulten, and
Yann R. Chemla.
Nucleic Acids Research, 41:2416-2427, 2013.
|
| 585. Mechanisms of SecM-mediated stalling in the ribosome.
James Gumbart, Eduard Schreiner, Daniel N. Wilson, Roland Beckmann, and Klaus
Schulten.
Biophysical Journal, 103:331-341, 2012.
|
| 578. Structural characterization of mRNA-tRNA translocation
intermediates.
Xabier Agirrezabala, Hstau Liao, Eduard Schreiner, Jie Fu, Rodrigo Ortiz-Meoz,
Klaus Schulten, Rachel Green, and Joachim Frank.
Proceedings of the National Academy of Sciences, USA,
109:6094-6099, 2012.
|
| 574. Recognition of methylated DNA through methyl-CpG binding domain
proteins.
Xueqing Zou, Wen Ma, Ilia Solov'yov, Christophe Chipot, and Klaus Schulten.
Nucleic Acids Research, 40:2747-2758, 2012.
|
| 567. Cytosine methylation alters DNA mechanical properties.
Philip M.D. Severin, Xueqing Zou, Hermann E. Gaub, and Klaus Schulten.
Nucleic Acids Research, 39:8740-8751, 2011.
|
| 558. Computational investigation of DNA detection using graphene
nanopores.
Chaitanya Sathe, Xueqing Zou, Jean-Pierre Leburton, and Klaus Schulten.
ACS Nano, 5:8842-8851, 2011.
|
| 554. Structural insights into cognate vs. near-cognate discrimination
during decoding.
Xabier Agirrezabala, Eduard Schreiner, Leonardo G. Trabuco, Jianlin Lei,
Rodrigo F. Ortiz-Meoz, Klaus Schulten, Rachel Green, and Joachim Frank.
EMBO Journal, 30:1497-1507, 2011.
|
| 553. Cryo-EM structure of the ribosome-SecYE complex in the membrane
environment.
Jens Frauenfeld, James Gumbart, Eli O. van der Sluis, Soledad Funes, Marco
Gartmann, Birgitta Beatrix, Thorsten Mielke, Otto Berninghausen, Thomas
Becker, Klaus Schulten, and Roland Beckmann.
Nature Structural & Molecular Biology, 18:614-621, 2011.
|
| 552. 3rd generation DNA sequencing with a nanopore.
Gregory Timp, Utkur Mirsaidov, Winston Timp, Jiwook Shim, Deqiang Wang,
Valentin Dimitrov, Jan Scrimgeour, Chunchen Lin, Jeffrey Comer, Anthony Ho,
Xueqing Zou, Aleksei Aksimentiev, and Klaus Schulten.
In Samir M. Iqbal and Rashid Bashir, editors, Nanopores: Sensing
and Fundamental Biological Interactions, chapter 12, pp. 287-312. Springer,
Berlin, 2011.
|
| 546. Molecular dynamics of EF-G during translocation.
Wen Li, Leonardo G. Trabuco, Klaus Schulten, and Joachim Frank.
PROTEINS: Structure, Function, and Bioinformatics,
79:1478-1486, 2011.
|
| 543. Viewing the mechanisms of translation through the computational
microscope.
James Gumbart, Eduard Schreiner, Leonardo G. Trabuco, Kwok-Yan Chan, and Klaus
Schulten.
In Joachim Frank, editor, Molecular Machines in Biology,
chapter 8, pp. 142-157. Cambridge University Press, 2011.
|
| 536. The role of L1 stalk-tRNA interaction in the ribosome elongation
cycle.
Leonardo G. Trabuco, Eduard Schreiner, John Eargle, Peter Cornish, Taekjip Ha,
Zaida Luthey-Schulten, and Klaus Schulten.
Journal of Molecular Biology, 402:741-760, 2010.
|
| 520. Recognition of the regulatory nascent chain TnaC by the ribosome.
Leonardo G. Trabuco, Christopher B Harrison, Eduard Schreiner, and Klaus
Schulten.
Structure, 18:627-637, 2010.
|
| 513. Structural insight into nascent polypeptide chain-mediated
translational stalling.
Birgit Seidelt, C. Axel Innis, Daniel N. Wilson, Marco Gartmann, Jean-Paul
Armache, Elizabeth Villa, Leonardo G. Trabuco, Thomas Becker, Thorsten
Mielke, Klaus Schulten, Thomas A. Steitz, and Roland Beckmann.
Science, 326:1412-1415, 2009.
|
| 512. Structure of monomeric yeast and mammalian Sec61 complexes
interacting with the translating ribosome.
Thomas Becker, Shashi Bhushan, Alexander Jarasch, Jean-Paul Armache, Soledad
Funes, Fabrice Jossinet, James Gumbart, Thorsten Mielke, Otto Berninghausen,
Klaus Schulten, Eric Westhof, Reid Gilmore, Elisabet C. Mandon, and Roland
Beckmann.
Science, 326:1369-1373, 2009.
|
| 498. Molecular Dynamics Flexible Fitting: A practical guide to combine
cryo-electron microscopy and X-ray crystallography.
Leonardo G. Trabuco, Elizabeth Villa, Eduard Schreiner, Christopher B.
Harrison, and Klaus Schulten.
Methods, 49:174-180, 2009.
|
| 487. Ribosome-induced changes in elongation factor Tu conformation
control GTP hydrolysis.
Elizabeth Villa, Jayati Sengupta, Leonardo G. Trabuco, Jamie LeBarron,
William T. Baxter, Tanvir R. Shaikh, Robert A. Grassucci, Poul Nissen,
Måns Ehrenberg, Klaus Schulten, and Joachim Frank.
Proceedings of the National Academy of Sciences, USA,
106:1063-1068, 2009.
|
| 484. Nanoelectromechanics of methylated DNA in a synthetic nanopore.
Utkur M. Mirsaidov, Winston Timp, Xueqing Zou, Valentin Dimitrov, Klaus
Schulten, Andrew P. Feinberg, and Greg Timp.
Biophysical Journal, 96:L32-L34, 2009.
|
| 473. Flexible fitting of atomic structures into electron microscopy maps
using molecular dynamics.
Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, and Klaus
Schulten.
Structure, 16:673-683, 2008.
|
| 451. Double stranded DNA dissociates into single strands when dragged
into a poor solvent.
Shuxun Cui, Jin Yu, Ferdinand Kühner, Klaus Schulten, and Hermann E. Gaub.
Journal of the American Chemical Society, 129:14710-14716,
2007.
|
| 448. How directional translocation is regulated in a DNA helicase motor.
Jin Yu, Taekjip Ha, and Klaus Schulten.
Biophysical Journal, 93:3783-3797, 2007.
|
| 432. Fluorescence-force spectroscopy maps two-dimensional reaction
landscape of the Holliday junction.
Sungchul Hohng, Ruobo Zhou, Michelle K. Nahas, Jin Yu, Klaus Schulten, David
M. J. Lilley, and Taekjip Ha.
Science, 318:279-283, 2007.
|
| 422. PcrA helicase, a prototype ATP-driven molecular motor.
Markus Dittrich and Klaus Schulten.
Structure, 14:1345-1353, 2006.
|
| 420. Structure-based model of the stepping motor of PcrA helicase.
Jin Yu, Taekjip Ha, and Klaus Schulten.
Biophysical Journal, 91:2097-2114, 2006.
|
| 418. PcrA helicase, a molecular motor studied from the electronic to the
functional level.
Markus Dittrich, Jin Yu, and Klaus Schulten.
Topics in Current Chemistry, 268:319-347, 2006.
|
| 411. Modeling DNA loops using the theory of elasticity.
Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Physical Review E, 73:031919, 2006.
(23 pages).
|
| 407. Simulation of the electric response of DNA translocation through a
semiconductor nanopore-capacitor.
Maria E. Gracheva, Anlin Xiong, Aleksei Aksimentiev, Klaus Schulten, Gregory
Timp, and Jean-Pierre Leburton.
Nanotechnology, 17:622-633, 2006.
|
| 406. Molecular dynamics simulations of the complete satellite tobacco
mosaic virus.
Peter L. Freddolino, Anton S. Arkhipov, Steven B. Larson, Alexander McPherson,
and Klaus Schulten.
Structure, 14:437-449, 2006.
|
| 399. Biomolecular modeling using parallel supercomputers.
Laxmikant V. Kale, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark
Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng.
In S. Aluru, editor, Handbook of Computational Molecular
Biology, pp. 34.1-34.43. Taylor and Francis, 2005.
|
| 398. Orientation discrimination of single stranded DNA inside the
α-hemolysin membrane channel.
Jerome Mathé, Aleksei Aksimentiev, David R. Nelson, Klaus Schulten, and
Amit Meller.
Proceedings of the National Academy of Sciences, USA,
102:12377-12382, 2005.
|
| 395. Beyond the gene chip.
J. B. Heng, A. Aksimentiev, C. Ho, V. Dimitrov, T. Sorsch, J. Miner,
W. Mansfield, K. Schulten, and G. Timp.
Bell Labs Technical Journal, 10:5-22, 2005.
|
| 391. Stretching DNA using an electric field in a synthetic nanopore.
J. B Heng, A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar,
K. Schulten, and G. Timp.
Nano Letters, 5:1883-1888, 2005.
|
| 388. Structural dynamics of the Lac repressor-DNA complex
revealed by a multiscale simulation.
Elizabeth Villa, Alexander Balaeff, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
102:6783-6788, 2005.
|
| 379. Conformational model of the Holliday junction transition deduced
from molecular dynamics simulations.
Jin Yu, Taekjip Ha, and Klaus Schulten.
Nucleic Acids Research, 32:6683-6695, 2004.
|
| 371. Microscopic kinetics of DNA translocation through synthetic
nanopores.
Aleksij Aksimentiev, Jiunn Benjamin Heng, Gregory Timp, and Klaus Schulten.
Biophysical Journal, 87:2086-2097, 2004.
|
| 370. Sizing DNA using a nanometer-diameter pore.
J. B. Heng, C. Ho, T. Kim, R. Timp, A. Aksimentiev, Y. V. Grinkova, S. Sligar,
K. Schulten, and G. Timp.
Biophysical Journal, 87:2905-2911, 2004.
|
| 362. Multi-scale method for simulating protein-DNA complexes.
Elizabeth Villa, Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Multiscale Modeling and Simulation, 2:527-553, 2004.
|
| 353. Modeling DNA loops using continuum and statistical mechanics.
Alexander Balaeff, Christophe R. Koudella, L. Mahadevan, and Klaus Schulten.
Philosophical Transactions of the Royal Society of London A. (Mathematical, Physical and Engineering Sciences), 362:1355-1371, 2004.
|
| 349. Structural basis for cooperative DNA binding by CAP and
Lac repressor.
Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Structure, 12:123-132, 2004.
|
| 290. Elastic rod model of a DNA loop in the lac operon.
Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Physical Review Letters, 83:4900-4903, 1999.
|
| 282. Probing the role of structural water in a duplex
oligodeoxyribonucleotide containing a water-mimicking base analogue.
Dorina Kosztin, Richard Gumport, and Klaus Schulten.
Nucleic Acids Research, 27:3550-3556, 1999.
|
| 253. Structure prediction of a complex between the chromosomal protein
HMG-D and DNA.
Alexander Balaeff, Mair E. A. Churchill, and Klaus Schulten.
PROTEINS: Structure, Function, and Genetics, 30:113-135, 1998.
|
| 243. Binding of the estrogen receptor to DNA: The role of waters.
Dorina Kosztin, Thomas C. Bishop, and Klaus Schulten.
Biophysical Journal, 73:557-570, 1997.
|
| 237. How hormone receptor-DNA binding affects nucleosomal DNA: The
role of symmetry.
Tom Connor Bishop, Dorina Kosztin, and Klaus Schulten.
Biophysical Journal, 72:2056-2067, 1997.
|
| 209. Molecular dynamics study of glucocorticoid receptor-DNA binding.
Thomas C. Bishop and Klaus Schulten.
PROTEINS: Structure, Function, and Genetics, 24:115-133, 1996.
|
| 186. Molecular dynamics study of a sequence specific protein-DNA
interaction.
Thomas C. Bishop and Klaus Schulten.
In G. Wipff, editor, Computational Approaches in Supramolecular
Chemistry, pp. 419-439. Kluwer Academic Publishers, Boston, 1994.
|
| 143. Molecular dynamics investigation of the interaction between DNA and
dystamycin.
Klaus Boehncke, Marco Nonella, Klaus Schulten, and Andrew H.-J. Wang.
Biochemistry, 30:5465-5475, 1991.
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