|
| 693. Dynamic behavior of trigger factor on the ribosome.
Julian Deeng, Kwok-Yan Chan, Eli O. van der Sluis, Lukas Bischoff, Otto
Berninghausen, Wei Han, James Gumbart, Klaus Schulten, Birgitta Beatrix, and
Roland Beckmann.
Journal of Molecular Biology, 428:3588-3602, 2016.
|
| 617. Generalized scalable multiple copy algorithms for molecular dynamics
simulations in NAMD.
Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C.
Gumbart, Yun Luo, Klaus Schulten, and Benoît Roux.
Computer Physics Communications, 185:908-916, 2014.
(PMC: PMC4059768) |
| 613. Rapid parameterization of small molecules using the Force Field
Toolkit.
Christopher G. Mayne, Jan Saam, Klaus Schulten, Emad Tajkhorshid, and James C.
Gumbart.
Journal of Computational Chemistry, 34:2757-2770, 2013.
(PMC: 3874408) |
| 604. Reconciling the roles of kinetic and thermodynamic factors in
membrane-protein insertion.
James C. Gumbart, Ivan Teo, Benoit Roux, and Klaus Schulten.
Journal of the American Chemical Society, 135:2291-2297, 2013.
(PMC: 3573731) |
| 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.
(PMC: 3400775) |
| 571. Symmetry-restrained flexible fitting for symmetric EM maps.
Kwok-Yan Chan, James Gumbart, Ryan McGreevy, Jean M. Watermeyer, B. Trevor
Sewell, and Klaus Schulten.
Structure, 19:1211-1218, 2011.
(PMC: 3412758) |
| 561. Free energy of nascent-chain folding in the translocon.
James Gumbart, Christophe Chipot, and Klaus Schulten.
Journal of the American Chemical Society, 133:7602-7607, 2011.
(PMC: 3100187) |
| 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.
(PMC: PMC3412285) |
| 550. Free-energy cost for translocon-assisted insertion of membrane
proteins.
James Gumbart, Christophe Chipot, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
108:3596-3601, 2011.
(PMC: PMC3048118) |
| 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.
|
| 541. Applications of the molecular dynamics flexible fitting method.
Leonardo G. Trabuco, Eduard Schreiner, James Gumbart, Jen Hsin, Elizabeth
Villa, and Klaus Schulten.
Journal of Structural Biology, 173:420-427, 2011.
(PMC: 3032011) |
| 519. Self-assembly of photosynthetic membranes.
Jen Hsin, Danielle E. Chandler, James Gumbart, Christopher B. Harrison, Melih
Sener, Johan Strumpfer, and Klaus Schulten.
ChemPhysChem, 11:1154-1159, 2010.
(PMC: 3086839) |
| 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.
(PMC: 2920595) |
| 509. Regulation of the protein-conducting channel by a bound ribosome.
James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, and
Klaus Schulten.
Structure, 17:1453-1464, 2009.
(PMC: 2778611) |
| 507. Membrane curvature induced by aggregates of LH2s and monomeric
LH1s.
Danielle E. Chandler, James Gumbart, John D. Stack, Christophe Chipot, and
Klaus Schulten.
Biophysical Journal, 97:2978-2984, 2009.
(PMC: 2784572) |
| 499. Protein-induced membrane curvature investigated through molecular
dynamics flexible fitting.
Jen Hsin, James Gumbart, Leonardo G. Trabuco, Elizabeth Villa, Pu Qian, C. Neil
Hunter, and Klaus Schulten.
Biophysical Journal, 97:321-329, 2009.
(PMC: 2711417) |
| 495. Molecular dynamics simulations of membrane channels and transporters.
Fatemeh Khalili-Araghi, James Gumbart, Po-Chao Wen, Marcos Sotomayor, Emad
Tajkhorshid, and Klaus Schulten.
Current Opinion in Structural Biology, 19:128-137, 2009.
(PMC: 2680122) |
| 477. Intrinsic curvature properties of photosynthetic proteins in
chromatophores.
Danielle Chandler, Jen Hsin, Christopher B. Harrison, James Gumbart, and Klaus
Schulten.
Biophysical Journal, 95:2822-2836, 2008.
(PMC: 2527265) |
| 476. The roles of pore ring and plug in the SecY protein-conducting
channel.
James Gumbart and Klaus Schulten.
Journal of General Physiology, 132:709-719, 2008.
(PMC: 2585858) |
| 450. Structural determinants of lateral gate opening in the protein
translocon.
James Gumbart and Klaus Schulten.
Biochemistry, 46:11147-11157, 2007.
|
| 410. Molecular dynamics studies of the archaeal translocon.
James Gumbart and Klaus Schulten.
Biophysical Journal, 90:2356-2367, 2006.
(PMC: 1403164) |
| 400. Scalable molecular dynamics with NAMD.
James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid,
Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and
Klaus Schulten.
Journal of Computational Chemistry, 26:1781-1802, 2005.
(PMC: 2486339)) |
| 397. Molecular dynamics simulations of proteins in lipid bilayers.
James Gumbart, Yi Wang, Alekseij Aksimentiev, Emad Tajkhorshid, and Klaus
Schulten.
Current Opinion in Structural Biology, 15:423-431, 2005.
(PMC: 2474857) |
