| Improved side‐chain torsion potentials for the Amber ff99SB protein force field K Lindorff‐Larsen, S Piana, K Palmo, P Maragakis, JL Klepeis, RO Dror, ... Proteins: Structure, Function, and Bioinformatics 78 (8), 1950-1958, 2010 | 5541 | 2010 |
| Atomic-level characterization of the structural dynamics of proteins DE Shaw, P Maragakis, K Lindorff-Larsen, S Piana, RO Dror, ... Science 330 (6002), 341-346, 2010 | 2021 | 2010 |
| Pathway and mechanism of drug binding to G-protein-coupled receptors RO Dror, AC Pan, DH Arlow, DW Borhani, P Maragakis, Y Shan, H Xu, ... Proceedings of the National Academy of Sciences 108 (32), 13118-13123, 2011 | 801 | 2011 |
| Systematic validation of protein force fields against experimental data K Lindorff-Larsen, P Maragakis, S Piana, MP Eastwood, RO Dror, ... PloS one 7 (2), e32131, 2012 | 761 | 2012 |
| Millisecond-scale molecular dynamics simulations on Anton DE Shaw, RO Dror, JK Salmon, JP Grossman, KM Mackenzie, JA Bank, ... Proceedings of the conference on high performance computing networking …, 2009 | 681 | 2009 |
| Activation mechanism of the β2-adrenergic receptor RO Dror, DH Arlow, P Maragakis, TJ Mildorf, AC Pan, H Xu, DW Borhani, ... Proceedings of the National Academy of Sciences 108 (46), 18684-18689, 2011 | 628 | 2011 |
| Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase P Maragakis, M Karplus Journal of molecular biology 352 (4), 807-822, 2005 | 373 | 2005 |
| Principles of conduction and hydrophobic gating in K+ channels MØ Jensen, DW Borhani, K Lindorff-Larsen, P Maragakis, V Jogini, ... Proceedings of the National Academy of Sciences 107 (13), 5833-5838, 2010 | 366 | 2010 |
| Structure and dynamics of an unfolded protein examined by molecular dynamics simulation K Lindorff-Larsen, N Trbovic, P Maragakis, S Piana, DE Shaw Journal of the American Chemical Society 134 (8), 3787-3791, 2012 | 284 | 2012 |
| Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins P Maragakis, K Lindorff-Larsen, MP Eastwood, RO Dror, JL Klepeis, ... The Journal of Physical Chemistry B 112 (19), 6155-6158, 2008 | 238 | 2008 |
| Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide W Ren, E Vanden-Eijnden, P Maragakis The Journal of chemical physics 123 (13), 2005 | 229 | 2005 |
| Carbon nanotube interaction with DNA G Lu, P Maragakis, E Kaxiras Nano letters 5 (5), 897-900, 2005 | 213 | 2005 |
| DNA nucleoside interaction and identification with carbon nanotubes S Meng, P Maragakis, C Papaloukas, E Kaxiras nano letters 7 (1), 45-50, 2007 | 202 | 2007 |
| Adaptive nudged elastic band approach for transition state calculation P Maragakis, SA Andreev, Y Brumer, DR Reichman, E Kaxiras The Journal of chemical physics 117 (10), 4651-4658, 2002 | 202 | 2002 |
| Picosecond to millisecond structural dynamics in human ubiquitin K Lindorff-Larsen, P Maragakis, S Piana, DE Shaw The Journal of Physical Chemistry B 120 (33), 8313-8320, 2016 | 128 | 2016 |
| A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories T Tu, CA Rendleman, DW Borhani, RO Dror, J Gullingsrud, MO Jensen, ... SC'08: Proceedings of the 2008 ACM/IEEE conference on Supercomputing, 1-12, 2008 | 105 | 2008 |
| Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise P Maragakis, F Ritort, C Bustamante, M Karplus, GE Crooks The Journal of chemical physics 129 (2), 2008 | 84 | 2008 |
| Gaussian-mixture umbrella sampling P Maragakis, A van der Vaart, M Karplus The Journal of Physical Chemistry B 113 (14), 4664-4673, 2009 | 76 | 2009 |
| Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09) DE Shaw, RO Dror, JK Salmon, JP Grossman, KM Mackenzie, JA Bank, ... ACM Press, 2009 | 72 | 2009 |
| Determination of DNA-base orientation on carbon nanotubes through directional optical absorbance S Meng, WL Wang, P Maragakis, E Kaxiras nano letters 7 (8), 2312-2316, 2007 | 70 | 2007 |
