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Huafeng Xu, Ph.D. - Publications

Affiliations: 
2001 Columbia University, New York, NY 
Area:
Theory of liquids, molecular dynamics and Monte Carlo simulations of condensed matter
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18 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Chen L, Wu Y, Wu C, Silveira A, Sherman W, Xu H, Gallicchio E. Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands. Journal of Chemical Information and Modeling. PMID 38147877 DOI: 10.1021/acs.jcim.3c01705  0.569
2023 Khuttan S, Azimi S, Wu JZ, Dick S, Wu C, Xu H, Gallicchio E. Taming multiple binding poses in alchemical binding free energy prediction: the β-cyclodextrin host-guest SAMPL9 blinded challenge. Physical Chemistry Chemical Physics : Pccp. PMID 37676233 DOI: 10.1039/d3cp02125d  0.554
2017 Pan AC, Xu H, Palpant T, Shaw DE. Quantitative characterization of the binding and unbinding of millimolar drug fragments with molecular dynamics simulations. Journal of Chemical Theory and Computation. PMID 28582625 DOI: 10.1021/Acs.Jctc.7B00172  0.337
2012 Dirks RM, Xu H, Shaw DE. Improving Sampling by Exchanging Hamiltonians with Efficiently Configured Nonequilibrium Simulations. Journal of Chemical Theory and Computation. 8: 162-71. PMID 26592879 DOI: 10.1021/Ct200464V  0.326
2012 Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE. Biomolecular simulation: a computational microscope for molecular biology. Annual Review of Biophysics. 41: 429-52. PMID 22577825 DOI: 10.1146/Annurev-Biophys-042910-155245  0.36
2012 Predescu C, Lippert RA, Eastwood MP, Ierardi D, Xu H, Jensen M, Bowers KJ, Gullingsrud J, Rendleman CA, Dror RO, Shaw DE. Computationally efficient molecular dynamics integrators with improved sampling accuracy Molecular Physics. 110: 967-983. DOI: 10.1080/00268976.2012.681311  0.355
2010 Agrafiotis DK, Xu H, Zhu F, Bandyopadhyay D, Liu P. Stochastic Proximity Embedding: Methods and Applications. Molecular Informatics. 29: 758-70. PMID 27464266 DOI: 10.1002/Minf.201000134  0.462
2009 Shenfeld DK, Xu H, Eastwood MP, Dror RO, Shaw DE. Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 80: 046705. PMID 19905480 DOI: 10.1103/Physreve.80.046705  0.308
2009 Shan Y, Seeliger MA, Eastwood MP, Frank F, Xu H, Jensen MØ, Dror RO, Kuriyan J, Shaw DE. A conserved protonation-dependent switch controls drug binding in the Abl kinase. Proceedings of the National Academy of Sciences of the United States of America. 106: 139-44. PMID 19109437 DOI: 10.1073/Pnas.0811223106  0.304
2009 Shenfeld DK, Xu H, Eastwood MP, Dror RO, Shaw DE. Publisher's Note: Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations [Phys. Rev. E80, 046705 (2009)] Physical Review E. 80. DOI: 10.1103/Physreve.80.049904  0.304
2008 Maragakis P, Lindorff-Larsen K, Eastwood MP, Dror RO, Klepeis JL, Arkin IT, Jensen MØ, Xu H, Trbovic N, Friesner RA, Iii AG, Shaw DE. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. The Journal of Physical Chemistry. B. 112: 6155-8. PMID 18311962 DOI: 10.1021/Jp077018H  0.345
2005 Xu H, Dill KA. Water's hydrogen bonds in the hydrophobic effect: a simple model. The Journal of Physical Chemistry. B. 109: 23611-7. PMID 16375338 DOI: 10.1021/Jp0526750  0.36
2002 Agrafiotis DK, Xu H. A self-organizing principle for learning nonlinear manifolds. Proceedings of the National Academy of Sciences of the United States of America. 99: 15869-72. PMID 12444256 DOI: 10.1073/Pnas.242424399  0.304
2002 Xu H, Stern HA, Berne BJ. Can water polarizability be ignored in hydrogen bond kinetics? Journal of Physical Chemistry B. 106: 2054-2060. DOI: 10.1021/Jp013426O  0.618
2001 Zhou R, Harder E, Xu H, Berne BJ. Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems Journal of Chemical Physics. 115: 2348-2358. DOI: 10.1063/1.1385159  0.64
2001 Xu H, Berne BJ. Hydrogen-bond kinetics in the solvation shell of a polypeptide Journal of Physical Chemistry B. 105: 11929-11932. DOI: 10.1021/Jp012749H  0.508
2000 Xu H, Berne BJ. Multicanonical jump walk annealing: An efficient method for geometric optimization Journal of Chemical Physics. 112: 2701-2708. DOI: 10.1063/1.480844  0.488
1999 Xu H, Berne BJ. Multicanonical jump walking: A method for efficiently sampling rough energy landscapes Journal of Chemical Physics. 110: 10299-10306. DOI: 10.1063/1.478963  0.492
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