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Ruhong Zhou - Publications

Affiliations: 
2000- IBM Thomas J. Watson Research Center, Yorktown Heights, NY, United States 
Area:
novel algorithms for computational biology and bioinformatics, protein folding dynamics, protein-protein interaction, and ligand-receptor binding mechanism
Website:
http://www.columbia.edu/cu/chemistry/adjunct-faculty-bios/zhou/adjunct.html
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53 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
2018 Weber JK, Kang SG, Zhou R. Rare Dissipative Transitions Punctuate the Initiation of Chemical Denaturation in Proteins. Biophysical Journal. 114: 812-821. PMID 29490243 DOI: 10.1016/j.bpj.2017.12.038  0.308
2017 Zhang L, Feng M, Zhou R, Luan B. Structural Perturbations on Huntingtin N17 Domain during its Folding on 2D-Nanomaterials. Nanotechnology. PMID 28649967 DOI: 10.1088/1361-6528/aa7ba5  0.323
2017 Gu Z, De Luna P, Yang Z, Zhou R. Structural influence of proteins upon adsorption to MoS2 nanomaterials: comparison of MoS2 force field parameters. Physical Chemistry Chemical Physics : Pccp. PMID 28079199 DOI: 10.1039/c6cp05260f  0.327
2016 Gu Z, Yang Z, Kang SG, Yang JR, Luo J, Zhou R. Robust Denaturation of Villin Headpiece by MoS2 Nanosheet: Potential Molecular Origin of the Nanotoxicity. Scientific Reports. 6: 28252. PMID 27312409 DOI: 10.1038/srep28252  0.384
2016 Xu Z, Zhang S, Weber JK, Luan B, Zhou R, Li J. Sequential protein unfolding through a carbon nanotube pore. Nanoscale. PMID 26899409 DOI: 10.1039/c6nr00410e  0.314
2016 Luan B, Huynh T, Zhou R. Potential Interference of Protein-Protein Interactions by Graphyne. The Journal of Physical Chemistry. B. PMID 26885561 DOI: 10.1021/acs.jpcb.5b11449  0.336
2015 Luan B, Huynh T, Li J, Zhou R. Nanomechanics of Protein Unfolding Outside a Generic Nanopore. Acs Nano. PMID 26655061 DOI: 10.1021/acsnano.5b04557  0.301
2015 Gu Z, Yang Z, Wang L, Zhou H, Jimenez-Cruz CA, Zhou R. The role of basic residues in the adsorption of blood proteins onto the graphene surface. Scientific Reports. 5: 10873. PMID 26034971 DOI: 10.1038/Srep10873  0.642
2014 Stirnemann G, Kang SG, Zhou R, Berne BJ. How force unfolding differs from chemical denaturation. Proceedings of the National Academy of Sciences of the United States of America. 111: 3413-8. PMID 24550471 DOI: 10.1073/Pnas.1400752111  0.516
2012 Xia Z, Das P, Shakhnovich EI, Zhou R. Collapse of unfolded proteins in a mixture of denaturants. Journal of the American Chemical Society. 134: 18266-74. PMID 23057830 DOI: 10.1021/Ja3031505  0.365
2012 Yang Z, Xiu P, Shi B, Hua L, Zhou R. Coherent microscopic picture for urea-induced denaturation of proteins. The Journal of Physical Chemistry. B. 116: 8856-62. PMID 22780326 DOI: 10.1021/jp304114h  0.757
2012 Flores SC, Bernauer J, Shin S, Zhou R, Huang X. Multiscale modeling of macromolecular biosystems. Briefings in Bioinformatics. 13: 395-405. PMID 22228511 DOI: 10.1093/Bib/Bbr077  0.405
2012 Li W, Zhou R, Mu Y. Salting effects on protein components in aqueous NaCl and urea solutions: toward understanding of urea-induced protein denaturation. The Journal of Physical Chemistry. B. 116: 1446-51. PMID 22216970 DOI: 10.1021/jp210769q  0.325
2011 Xiu P, Yang Z, Zhou B, Das P, Fang H, Zhou R. Urea-induced drying of hydrophobic nanotubes: comparison of different urea models. The Journal of Physical Chemistry. B. 115: 2988-94. PMID 21384841 DOI: 10.1021/Jp108303Q  0.336
2011 Zhou R, Li J, Hua L, Yang Z, Berne BJ. Comment on "urea-mediated protein denaturation: a consensus view". The Journal of Physical Chemistry. B. 115: 1323-6; discussion 1. PMID 21247088 DOI: 10.1021/Jp105160A  0.762
2010 Morrone JA, Zhou R, Berne BJ. Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls. Journal of Chemical Theory and Computation. 6: 1798-804. PMID 26615840 DOI: 10.1021/Ct100054K  0.508
2010 Gao M, She ZS, Zhou R. Key residues that play a critical role in urea-induced lysozyme unfolding. The Journal of Physical Chemistry. B. 114: 15687-93. PMID 21053934 DOI: 10.1021/jp1052453  0.362
2010 Morrone JA, Zhou R, Berne BJ. Molecular dynamics with multiple time scales: How to avoid pitfalls Journal of Chemical Theory and Computation. 6: 1798-1804. DOI: 10.1021/ct100054k  0.465
2009 Zangi R, Zhou R, Berne BJ. Urea's action on hydrophobic interactions. Journal of the American Chemical Society. 131: 1535-41. PMID 19123816 DOI: 10.1021/Ja807887G  0.54
2009 Berne BJ, Weeks JD, Zhou R. Dewetting and hydrophobic interaction in physical and biological systems. Annual Review of Physical Chemistry. 60: 85-103. PMID 18928403 DOI: 10.1146/Annurev.Physchem.58.032806.104445  0.47
2008 Hua L, Zhou R, Thirumalai D, Berne BJ. Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proceedings of the National Academy of Sciences of the United States of America. 105: 16928-33. PMID 18957546 DOI: 10.1073/Pnas.0808427105  0.79
2008 Krone MG, Hua L, Soto P, Zhou R, Berne BJ, Shea JE. Role of water in mediating the assembly of Alzheimer amyloid-beta Abeta16-22 protofilaments. Journal of the American Chemical Society. 130: 11066-72. PMID 18661994 DOI: 10.1021/Ja8017303  0.75
2008 Zhou R, Eleftheriou M, Hon CC, Germain RS, Royyuru AK, Berne BJ. Massively parallel molecular dynamics simulations of lysozyme unfolding Ibm Journal of Research and Development. 52: 19-30. DOI: 10.1147/Rd.521.0019  0.562
2007 Hua L, Huang X, Liu P, Zhou R, Berne BJ. Nanoscale dewetting transition in protein complex folding. The Journal of Physical Chemistry. B. 111: 9069-77. PMID 17608515 DOI: 10.1021/Jp0704923  0.785
2007 Huang X, Hagen M, Kim B, Friesner RA, Zhou R, Berne BJ. Replica exchange with solute tempering: efficiency in large scale systems. The Journal of Physical Chemistry. B. 111: 5405-10. PMID 17439169 DOI: 10.1021/Jp068826W  0.767
2007 Zhou R, Eleftheriou M, Royyuru AK, Berne BJ. Destruction of long-range interactions by a single mutation in lysozyme. Proceedings of the National Academy of Sciences of the United States of America. 104: 5824-9. PMID 17389393 DOI: 10.1073/Pnas.0701249104  0.459
2007 Zhou R. Replica exchange molecular dynamics method for protein folding simulation Methods in Molecular Biology (Clifton, N.J.). 350: 205-223. PMID 16957325  0.327
2006 Liu P, Huang X, Zhou R, Berne BJ. Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent. The Journal of Physical Chemistry. B. 110: 19018-22. PMID 16986898 DOI: 10.1021/Jp060365R  0.705
2006 Hua L, Huang X, Zhou R, Berne BJ. Dynamics of water confined in the interdomain region of a multidomain protein. The Journal of Physical Chemistry. B. 110: 3704-11. PMID 16494427 DOI: 10.1021/Jp055399Y  0.766
2005 Huang X, Zhou R, Berne BJ. Drying and hydrophobic collapse of paraffin plates. The Journal of Physical Chemistry. B. 109: 3546-52. PMID 16851392 DOI: 10.1021/Jp045520L  0.632
2005 Liu P, Huang X, Zhou R, Berne BJ. Observation of a dewetting transition in the collapse of the melittin tetramer. Nature. 437: 159-62. PMID 16136146 DOI: 10.1038/Nature03926  0.676
2005 Zhou R. Protein Folding with the Parallel Replica Exchange Molecular Dynamics Method Parallel Computing For Bioinformatics and Computational Biology: Models, Enabling Technologies, and Case Studies. 395-425. DOI: 10.1002/0471756504.ch17  0.326
2004 Zhou R, Huang X, Margulis CJ, Berne BJ. Hydrophobic collapse in multidomain protein folding. Science (New York, N.Y.). 305: 1605-9. PMID 15361621 DOI: 10.1126/Science.1101176  0.758
2004 Zhou R. Exploring the protein folding free energy landscape: Coupling replica exchange method with P3ME/RESPA algorithm Journal of Molecular Graphics and Modelling. 22: 451-463. PMID 15099840 DOI: 10.1016/j.jmgm.2003.12.011  0.343
2004 Zhou R, Krilov G, Berne BJ. Comment on "can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?" The Poisson-Boltzmann equation Journal of Physical Chemistry B. 108: 7528-7530. DOI: 10.1021/Jp037812C  0.707
2003 Zhou R. Free energy landscape of protein folding in water: Explicit vs. implicit solvent Proteins: Structure, Function and Genetics. 53: 148-161. PMID 14517967 DOI: 10.1002/prot.10483  0.307
2003 Zhou R, Silverman BD, Royyuru AK, Athma P. Spatial profiling of protein hydrophobicity: native vs. decoy structures. Proteins. 52: 561-72. PMID 12910456 DOI: 10.1002/prot.10419  0.303
2003 Kaminski GA, Friesner RA, Zhou R. A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations. Journal of Computational Chemistry. 24: 267-76. PMID 12548718 DOI: 10.1002/Jcc.10170  0.523
2002 Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YX, Murphy RB, Zhou R, Halgren TA. Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. Journal of Computational Chemistry. 23: 1515-31. PMID 12395421 DOI: 10.1002/Jcc.10125  0.756
2002 Zhou R, Berne BJ. Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water? Proceedings of the National Academy of Sciences of the United States of America. 99: 12777-82. PMID 12242327 DOI: 10.1073/Pnas.142430099  0.502
2001 Zhou R, Berne BJ, Germain R. The free energy landscape for beta hairpin folding in explicit water. Proceedings of the National Academy of Sciences of the United States of America. 98: 14931-6. PMID 11752441 DOI: 10.1073/Pnas.201543998  0.498
2001 Allen F, Almasi G, Andreoni W, Beece D, Berne BJ, Bright A, Brunheroto J, Cascaval C, Castanos J, Coteus P, Crumley P, Curioni A, Denneau M, Donath W, Eleftheriou M, ... ... Zhou R, et al. Blue Gene: A vision for protein science using a petaflop supercomputer Ibm Systems Journal. 40: 310-327. DOI: 10.1147/sj.402.0310  0.613
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  0.765
2001 Zhou R, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy RM. New linear interaction method for binding affinity calculations using a continuum solvent model Journal of Physical Chemistry B. 105: 10388-10397. DOI: 10.1021/Jp011480Z  0.654
1999 Banks JL, Kaminski GA, Zhou R, Mainz DT, Berne BJ, Friesner RA. Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model The Journal of Chemical Physics. 110: 741-754. DOI: 10.1063/1.478043  0.6
1999 Stern HA, Kaminski GA, Banks JL, Zhou R, Berne BJ, Friesner RA. Fluctuating charge, polarizable dipole, and combined models: Parameterization from ab initio quantum chemistry Journal of Physical Chemistry B. 103: 4730-4737. DOI: 10.1021/Jp984498R  0.724
1999 Friedrichs M, Zhou R, Edinger SR, Friesner RA. Poisson−Boltzmann Analytical Gradients for Molecular Modeling Calculations The Journal of Physical Chemistry B. 103: 3057-3061. DOI: 10.1021/jp982513m  0.429
1997 Figueirido F, Levy RM, Zhou R, Berne BJ. Erratum: “Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators” [J. Chem. Phys. 106, 9835 (1997)] The Journal of Chemical Physics. 107: 7002-7002. DOI: 10.1063/1.475334  0.462
1997 Zhou R, Berne BJ. Smart walking: A new method for Boltzmann sampling of protein conformations The Journal of Chemical Physics. 107: 9185-9196. DOI: 10.1063/1.475210  0.471
1997 Figueirido F, Levy RM, Zhou R, Berne BJ. Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators The Journal of Chemical Physics. 106: 9835-9849. DOI: 10.1063/1.474115  0.453
1996 Stuart SJ, Zhou R, Berne BJ. Molecular dynamics with multiple time scales: The selection of efficient reference system propagators The Journal of Chemical Physics. 105: 1426-1436. DOI: 10.1063/1.472005  0.668
1996 Zhou R, Stuart SJ, Berne BJ. Molecular dynamics for nonequilibrium systems in which there are a small number of very hot particles in a cold bath: Reference system propagator methods The Journal of Chemical Physics. 105: 235-239. DOI: 10.1063/1.471868  0.665
1995 Zhou R, Berne BJ. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems The Journal of Chemical Physics. 103: 9444-9459. DOI: 10.1063/1.470006  0.503
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