| 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 | 3244 | 2006 |
| Biomolecular simulation: a computational microscope for molecular biology RO Dror, RM Dirks, JP Grossman, H Xu, DE Shaw Annual review of biophysics 41 (1), 429-452, 2012 | 1258 | 2012 |
| 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 | 826 | 2011 |
| 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 | 639 | 2011 |
| A conserved protonation-dependent switch controls drug binding in the Abl kinase Y Shan, MA Seeliger, MP Eastwood, F Frank, H Xu, MØ Jensen, RO Dror, ... Proceedings of the National Academy of Sciences 106 (1), 139-144, 2009 | 293 | 2009 |
| Hydrogen-bond kinetics in the solvation shell of a polypeptide H Xu, BJ Berne The Journal of Physical Chemistry B 105 (48), 11929-11932, 2001 | 247 | 2001 |
| Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody AG Schmidt, H Xu, AR Khan, T O’Donnell, S Khurana, LR King, ... Proceedings of the National Academy of Sciences 110 (1), 264-269, 2013 | 246 | 2013 |
| Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery TS Lee, BK Allen, TJ Giese, Z Guo, P Li, C Lin, TD McGee Jr, ... Journal of Chemical Information and Modeling 60 (11), 5595-5623, 2020 | 242 | 2020 |
| 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 | 242 | 2008 |
| Can water polarizability be ignored in hydrogen bond kinetics? H Xu, HA Stern, BJ Berne The Journal of Physical Chemistry B 106 (8), 2054-2060, 2002 | 238 | 2002 |
| Best practices for alchemical free energy calculations [article v1. 0] ASJS Mey, BK Allen, HEB Macdonald, JD Chodera, DF Hahn, M Kuhn, ... Living journal of computational molecular science 2 (1), 2020 | 203 | 2020 |
| Mechanism of Na+/H+ antiporting IT Arkin, H Xu, MØ Jensen, E Arbely, ER Bennett, KJ Bowers, E Chow, ... Science 317 (5839), 799-803, 2007 | 181 | 2007 |
| Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems R Zhou, E Harder, H Xu, BJ Berne The Journal of chemical physics 115 (5), 2348-2358, 2001 | 158 | 2001 |
| A self-organizing principle for learning nonlinear manifolds DK Agrafiotis, H Xu Proceedings of the National Academy of Sciences 99 (25), 15869-15872, 2002 | 129 | 2002 |
| Quantitative characterization of the binding and unbinding of millimolar drug fragments with molecular dynamics simulations AC Pan, H Xu, T Palpant, DE Shaw Journal of chemical theory and computation 13 (7), 3372-3377, 2017 | 127 | 2017 |
| Proceedings of the 2006 ACM/IEEE Conference on Supercomputing KJ Bowers, E Chow, H Xu, RO Dror, MP Eastwood, BA Gregersen, ... ACM, 2006 | 104 | 2006 |
| Scalable algorithms for molecular dynamics simulations on commodity clusters JB Kevin, C Edmond, X Huafeng, OD Ron, PE Michael, AG Brent, LK John, ... Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), 11-17, 2006 | 99 | 2006 |
| Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations DK Shenfeld, H Xu, MP Eastwood, RO Dror, DE Shaw Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 80 (4 …, 2009 | 98 | 2009 |
| Method, system, and computer program product for representing object relationships in a multidimensional space DK Agrafiotis, DN Rassokhin, VS Lobanov, FR Salemme US Patent 7,139,739, 2006 | 94 | 2006 |
| Dynamic control of slow water transport by aquaporin 0: implications for hydration and junction stability in the eye lens MØ Jensen, RO Dror, H Xu, DW Borhani, IT Arkin, MP Eastwood, ... Proceedings of the National Academy of Sciences 105 (38), 14430-14435, 2008 | 93 | 2008 |
