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Huafeng Xu
Huafeng Xu
Atommap Corporation
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Title
Cited by
Cited by
Year
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
29632006
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
12192012
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
7982011
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
7972011
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
6252011
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
6252011
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
2892009
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
2452001
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
2412013
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
2382008
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
2362002
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
2052020
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
1802007
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
1702020
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
1532001
A self-organizing principle for learning nonlinear manifolds
DK Agrafiotis, H Xu
Proceedings of the National Academy of Sciences 99 (25), 15869-15872, 2002
1302002
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
1182017
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 80 (4), 046705, 2009
952009
Proceedings of the 2006 ACM/IEEE Conference on Supercomputing
KJ Bowers, E Chow, H Xu, RO Dror, MP Eastwood, BA Gregersen, ...
ACM, 2006
942006
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
932006
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