| Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy RA Friesner, JL Banks, RB Murphy, TA Halgren, JJ Klicic, DT Mainz, ... Journal of medicinal chemistry 47 (7), 1739-1749, 2004 | 9270 | 2004 |
| 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 | 5533 | 2010 |
| Scalable algorithms for molecular dynamics simulations on commodity clusters KJ Bowers, E Chow, H Xu, RO Dror, MP Eastwood, BA Gregersen, ... Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, 84-es, 2006 | 2997 | 2006 |
| A hierarchical approach to all‐atom protein loop prediction MP Jacobson, DL Pincus, CS Rapp, TJF Day, B Honig, DE Shaw, ... Proteins: Structure, Function, and Bioinformatics 55 (2), 351-367, 2004 | 2231 | 2004 |
| How fast-folding proteins fold K Lindorff-Larsen, S Piana, RO Dror, DE Shaw Science 334 (6055), 517, 2011 | 2020 | 2011 |
| 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 | 2017 | 2010 |
| PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results SL Dixon, AM Smondyrev, EH Knoll, SN Rao, DE Shaw, RA Friesner Journal of computer-aided molecular design 20, 647-671, 2006 | 1291 | 2006 |
| Biomolecular simulation: a computational microscope for molecular biology RO Dror, RM Dirks, JP Grossman, H Xu, DE Shaw Annual review of biophysics 41, 429-452, 2012 | 1230 | 2012 |
| Anton, a special-purpose machine for molecular dynamics simulation DE Shaw, MM Deneroff, RO Dror, JS Kuskin, RH Larson, JK Salmon, ... Communications of the ACM 51 (7), 91-97, 2008 | 965 | 2008 |
| Long-timescale molecular dynamics simulations of protein structure and function JL Klepeis, K Lindorff-Larsen, RO Dror, DE Shaw Current opinion in structural biology 19 (2), 120-127, 2009 | 923 | 2009 |
| Structure and dynamics of the M3 muscarinic acetylcholine receptor AC Kruse, J Hu, AC Pan, DH Arlow, DM Rosenbaum, E Rosemond, ... Nature 482 (7386), 552-556, 2012 | 910 | 2012 |
| Structure and function of an irreversible agonist-β2 adrenoceptor complex DM Rosenbaum, C Zhang, JA Lyons, R Holl, D Aragao, DH Arlow, ... Nature 469 (7329), 236-240, 2011 | 910 | 2011 |
| The dynamic process of β2-adrenergic receptor activation R Nygaard, Y Zou, RO Dror, TJ Mildorf, DH Arlow, A Manglik, AC Pan, ... Cell 152 (3), 532-542, 2013 | 884 | 2013 |
| How robust are protein folding simulations with respect to force field parameterization? S Piana, K Lindorff-Larsen, DE Shaw Biophysical journal 100 (9), L47-L49, 2011 | 856 | 2011 |
| A detailed and flexible cycle-accurate network-on-chip simulator N Jiang, DU Becker, G Michelogiannakis, J Balfour, B Towles, DE Shaw, ... 2013 IEEE international symposium on performance analysis of systems and …, 2013 | 849 | 2013 |
| Developing a molecular dynamics force field for both folded and disordered protein states P Robustelli, S Piana, DE Shaw Proceedings of the National Academy of Sciences 115 (21), E4758-E4766, 2018 | 814 | 2018 |
| 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 | 802 | 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 | 760 | 2012 |
| Water dispersion interactions strongly influence simulated structural properties of disordered protein states S Piana, AG Donchev, P Robustelli, DE Shaw The journal of physical chemistry B 119 (16), 5113-5123, 2015 | 728 | 2015 |
| Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer DE Shaw, JP Grossman, JA Bank, B Batson, JA Butts, JC Chao, ... SC'14: Proceedings of the International Conference for High Performance …, 2014 | 696 | 2014 |
