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 |
0.571 |
|
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 |
0.557 |
|
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 |
0.338 |
|
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 |
0.493 |
|
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