2000 – 2010
Title Heading link
2010
150. W. Lee, X. Zeng, H.-X. Zhou, V. Bennett, W. Yang, and P. E. Marszalek (2010). Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations. J. Biol. Chem. 285, 38167-38172.pdf
149. M. Sharma, M. Yi, H. Dong, H. Qin, E. Peterson, D. D. Busath, H.-X. Zhou, and T. A. Cross (2010). Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer. Science 330, 509-512.pdf Supporting Material
148. H.-X. Zhou (2010). Speeding up in a crowd. Physics 3, 77.pdf.
147. H.-X. Zhou (2010). Diffusion-influenced transport of ions across a transmembrane channel with an internal binding site. J. Phys. Chem. Lett. 1, 1973-1976.pdf
146. H. Dong, S. Qin, and H.-X. Zhou (2010). Effects of macromolecular crowding on protein conformational changes. PLoS Comput. Biol. 6, e1000833.pdf
145. S. Qin and H.-X. Zhou (2010). Selection of near-native poses in CAPRI rounds 13-19. Proteins 78, 3166-3173.pdf
144. H.-X. Zhou (2010). Rate theories for biologists. Q. Rev. Biophys. 43, 219-293.pdf
143. H. Tjong and H.-X. Zhou (2010). The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe. Biophys. J. 98, 2273-2280.pdf
142. S. Qin and H.-X. Zhou (2010). Generalized fundamental measure theory for atomistic modeling of macromolecular crowding. Phys. Rev. E 81, 031919.pdf Supplementary Information
141. H.-X. Zhou (2010). From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions. Biophys. J. 98, L15-L17.pdf Supporting Material
140. S. Qin, D. D. L. Minh, J. A. McCammon, and H.-X. Zhou (2010). Method to predict crowding effects by postprocessing molecular dynamics trajectories: application to the flap dynamics of HIV-1 protease. J. Phys. Chem. Lett. 1, 107-110.pdf Faculty of 1000 Evaluation
139. H.-X. Zhou and J. A. McCammon (2010). The gates of ion channels and enzymes. Trends Biochem. Sci. 35, 179-185.pdf
138. X. Zeng, H. Hu, H.-X. Zhou, P. E. Marszalek, and W. Yang (2010). Equilibrium sampling for biomolecules under mechanical tension. Biophys. J. 98, 733-740.pdf
137. A. Bazavov, B. A. Berg, and H.-X. Zhou (2010). Application of biased Metropolis algorithms: from protons to proteins. Math. Comput. Simul. 80, 1056-1067.pdf
2009
136. A. W. Maniccia, W. Yang, J. A. Johnson, S. Li, H. Tjong, H.-X. Zhou, L. A. Shaket, and J. J. Yang (2009). Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins. PMC Biophysics 2:11.pdf
135. M. Yi, T. A. Cross, and H.-X. Zhou (2009). Conformational heterogeneity of the M2 proton channel and a structural model for channel activation. Proc. Natl. Acad. Sci. USA 106, 13311-13316.pdf Supporting Figures Supporting Text.
134. J. Batra, K. Xu, S. Qin, and H.-X. Zhou (2009). Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequences. Biophys. J. 97, 906-911.pdf
133. S. Qin and H.-X. Zhou (2009). Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability. Biophys. J. 97, 12-19.pdf Faculty of 1000 Evaluation
132. S. Qin and H.-X. Zhou (2009). Dissection of the high rate constant for the binding of a ribotoxin to the ribosome. Proc. Natl. Acad. Sci. USA 106, 6974-7979.pdf Supporting Information Commentary
131. H.-X. Zhou and M. K. Gilson (2009). Theory of free energy and entropy in noncovalent binding. Chem. Rev. 109, 4092-4107.pdf Supporting Information
130. J. Batra, K. Xu, and H.-X. Zhou (2009). Nonaddtive effects of mixed crowding on protein stability. Proteins 77, 133-138.pdf
129. H.-X. Zhou (2009). Crowding effects of membrane proteins. J. Phys. Chem. B 113, 7995-8005.pdf
128. G. Schreiber, G. Haran, and H.-X. Zhou (2009). Fundamental aspects of protein-protein association kinetics. Chem. Rev. 109, 839-860.pdf
127. G.-C. Dong, P.-H. Chuang, K.-c. Chang, P.-s. Jan, P.-I. Hwang, H.-B. Wu, M. Yi, H.-X. Zhou, and H. M. Chen (2009). Blocking effect of an immuno-suppressive agent, cynarin, on CD28 of T-Cell receptor. Pharm. Res. 26, 375-381.pdf
2008
126. J.-M. Yuan, C.-L. Chyan, H.-X. Zhou, T.-Y. Chung, H. Peng, G. Ping, and G. Yang (2008). The effects of macromolecular crowding on the mechanical stability of protein molecules. Protein Sci. 17, 2156-2166.pdf
125. S. Li, W. Yang, A. W. Maniccia, D. Barrow Jr., H. Tjong, H.-X. Zhou, and J. J. Yang (2008). Rational design of a conformation switchable Ca2+ and Tb3+ binding protein without using multiple coupled metal binding sites. FEBS J. 275, 5048-5061.pdf
124. H.-X. Zhou (2008). The debut of PMC Biophysics. PMC Biophysics 1, 1.pdf
123. H. Tjong and H.-X. Zhou (2008). Accurate calculations of binding, folding, and transfer free energies by a scaled generalized Born method. J. Chem. Theory Comput. 4, 1733-1744.pdf
122. M. Yi, H. Nymeyer, and H.-X. Zhou (2008). Test of the Gouy-Chapman theory for a charged lipid membrane against explicit-solvent molecular dynamics simulations. Phys. Rev. Lett. 101, 038103.pdf Faculty of 1000 Evaluation
121. M. Yi, T. A. Cross, and H.-X. Zhou (2008). A secondary gate as a mechanism for inhibition of the M2 proton channel by amantadine. J. Phys. Chem. B 112, 7977-7979.pdf
120. H.-X. Zhou (2008). A minimum-reaction-flux solution to master-equation models of protein folding. J. Chem. Phys. 128, 195104.pdf
119. H.-X. Zhou, S. Qin, and H. Tjong (2008). Modeling protein-protein and protein-nucleic acid interactions: structure, thermodynamics, and kinetics. Annu. Report Comput. Chem. 4, 67-87.pdf
118. H.-X. Zhou (2008). Effect of mixed macromolecular crowding agents on protein folding. Proteins 72, 1109-1113.pdf
117. M. Yi, H. Tjong, and H.-X. Zhou (2008). Spontaneous conformational change and toxin binding in α7 nicotinic acetylcholine receptor: insight into channel activation and inhibition. Proc. Natl. Acad. Sci. 105, 8280-8285.pdf
116. H. Tjong and H.-X. Zhou (2008). Prediction of protein solubility from calculation of transfer free energy. Biophys. J. 95, 2601-2609.pdf.
115. R. Alsallaq and H.-X. Zhou (2008). Protein association with circular DNA: rate enhancement by nonspecific binding. J. Chem. Phys. 128, 115108.pdf
114. H. Tjong and H.-X. Zhou (2008). On the dielectric boundary in Poisson-Boltzmann calculations. J. Chem. Theory Comput. 4, 507-514.pdf
113. H.-X. Zhou, G. Rivas, and A. P. Minton (2008). Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu. Rev. Biophys. 37, 375-397.pdf
112. H.-X. Zhou (2008). Calculation of free-energy differences and potentials of mean force by a multi-energy gap method. J. Chem. Phys. 128, 114104.pdf
111. C. Li, M. Yi, J. Hu, H.-X. Zhou, and T. A. Cross (2008). Solid-state NMR and MD simulations of the anti-viral drug amantadine solubilized in DMPC bilayers. Biophys. J. 94, 1295-1302.pdf
110. H. Nymeyer and H.-X. Zhou (2008). A Method to determine dielectric constants in non-homogeneous systems: application to biological membranes. Biophys. J. 94, 1185-1193.pdf
109. W. Yang, H. Nymeyer, H.-X. Zhou, B. A. Berg, and R. Bruschweiler (2008). Quantitative computer simulations of biomolecules: a snapshot. J. Comput. Chem. 29, 668-672.pdf
108. R. Alsallaq and H.-X. Zhou (2008). Electrostatic rate enhancement and transient complex of protein-protein association. Proteins 71, 320-335.pdf
107. S. Qin and H.-X. Zhou (2008). Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II. J. Phys. Chem. B 112, 5955-5960.pdf
106. H.-X. Zhou (2008). Protein folding in confined and crowded environments. Arch. Biochem. Biophys., 469, 76-82.pdf
2007
105. H.-X. Zhou (2007). Helix formation inside a nanotube: possible influence of backbone-water hydrogen bonding by the confining surface through modulation of water activity. J. Chem. Phys. 127, 245101.pdf
104. N. Bhattacharya, M. Yi, H.-X. Zhou, and T. Logan (2007). Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR. J. Mol. Biol. 374, 977-992.pdf
103. S. Qin and H.-X. Zhou (2007). A holistic approach to protein docking. Proteins 69, 743-749.pdf
102. S. Qin and H.-X. Zhou (2007). meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformaticss 23, 3386-3387.pdf
101. H.-X. Zhou and S. Qin (2007). Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics 23, 2203-2209.pdf
100. H. Tjong and H.-X. Zhou (2007). GBr6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation. J. Chem. Phys. 126, 195102.pdf
99. H. Tjong, S. Qin, and H.-X. Zhou (2007). PI2PE: protein interface/interior prediction engine. Nucl. Acids Res. 35, W357-W362.pdf
98. S. Qin and H.-X. Zhou (2007). Do electrostatic interactions destabilize protein-nucleic acid binding? Biopolymers 86, 112-118.pdf
97. H. Tjong and H.-X. Zhou (2007). GBr6: a parameterization-free, accurate, analytical generalized Born method. J. Phys. Chem. B 111, 3055-3061.pdf
96. R. Alsallaq and H.-X. Zhou (2007). Prediction of protein-protein association rates from a transition-state theory. Structure 15, 215-224.pdf Faculty of 1000 Evaluation
95. H. Tjong and H.-X. Zhou (2007). DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucl. Acids Res. 35, 1465-1477.pdf
94. M. K. Gilson and H.-X. Zhou (2007). Calculation of protein-ligand binding affinities. Annu. Rev. Biophys. Biomol. Struct. 36, 21-42.E-print
93. R. Alsallaq and H.-X. Zhou (2007). Energy landscape and transition state of protein-protein association. Biophys. J. 92, 1486-1502.pdf
2006
92. H. Tjong and H.-X. Zhou (2006). The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations. J. Chem. Phys. 125, 206101.pdf
91. H.-X. Zhou (2006). Quantitative relation between intermolecular and intramolecular binding of Pro-rich peptides to SH3 domains. Biophys. J. 91, 3170-3181.pdf
90. X. Huang and H.-X. Zhou (2006). Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations. Biophys. J. 91, 2451-2463.pdf
89. F. Dong and H.-X. Zhou (2006). Electrostatic contribution to the binding stability of protein-protein complexes. Proteins 65, 87-102.pdf
88. J. Hu, R. Fu, K. Nishimura, L. Zhang, H.-X. Zhou, D. D. Busath, V. Vijayvergiya, and T. A. Cross (2006). Histidines, heart of the hydrogen ion channel from influenza A virus: toward an understanding of conductance and proton selectivity. Proc. Natl. Acad. Sci. USA 103, 6865-6870.pdf
2005
87. H.-X. Zhou (2005). How do biomolecular systems speed up and regulate rates? Phys. Biol. 2, R1-R25.Physical Biology pdf
86. B. A. Berg and H.-X. Zhou (2005). Rugged Metropolis sampling with simultaneous updating of two dynamical variables. Phys. Rev. E 72, 016712.pdf
85. H. Chen and H.-X. Zhou (2005). Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucl. Acids Res. 33, 3193-3199.pdf
84. D. S. Spencer, K. Xu, T. M. Logan, and H.-X. Zhou (2005). Effects of pH, salt, and macromolecular crowding on the stability of FK506-binding protein: an integrated experimental and theoretical study. J. Mol. Biol. 351, 219-232.
83. H. Chen and H.-X. Zhou (2005). Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 61, 21-35.pdf
82. H.-X. Zhou (2005). Interactions of macromolecules with salt ions: an electrostatic theory for the Hofmeister effect. Proteins 61, 69-78.pdf
81. A. D. J. van Dijk , S. J. de Vries, C. Dominguez, H. Chen, H.-X. Zhou, and A. M. J. J. Bonvin (2005). Data-driven docking: HADDOCK’s adventures in CAPRI. Proteins 60, 232-238.pdf
80. X. Huang, F. Dong, and H.-X. Zhou (2005). Electrostatic recognition and induced fit in the k-PVIIA toxin binding to Shaker potassium channel. J. Am. Chem. Soc 127, 6836-6849.pdf
79. H.-X. Zhou (2005). A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstacles. Biophys. J. 88, 1608-1615.pdf
2004
78. H.-X. Zhou and A. Szabo (2004). Enhancement of association rates by nonspecific binding to DNA and cell membranes. Phys. Rev. Lett. 93, 178101.pdf
77. H.-X. Zhou (2004). Polymer models of protein stability, folding, and interactions. Biochemistry 43, 2141-2154.pdf
76. H.-X. Zhou (2004). Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins. Acc. Chem. Res. 37, 123-130.pdf
75. H.-X. Zhou (2004). Protein folding and binding in confined spaces and in crowded solutions. J. Mol. Recog. 17, 368-375.pdf
74. H.-X. Zhou (2004). Improving the understanding of human genetic diseases through predictions of protein structures and protein-protein interaction sites. Curr. Med. Chem. 11, 539-549.pdf
2003
73. H.-X. Zhou (2003). How often does the myristoylated N-terminal latch of c-Abl come off? FEBS Lett. 552, 160-162.pdf
72. H.-X. Zhou (2003). Effect of backbone cyclization on protein folding stability: chain entropies of both the unfolded and the folded states are restricted. J. Mol. Biol. 332, 257-264.reprint
71. H.-X. Zhou (2003). Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experiment. Protein Sci. 12, 2379-2382.pdf
70. H.-X. Zhou (2003). Effect of catenation on protein folding stability. J. Am. Chem. Soc. 125, 9280-9281.pdf Faculty of 1000 Evaluation
69. H.-X. Zhou (2003). Quantitative account of the enhanced affinity of two linked scFvs specific for different epitopes on the same antigen. J. Mol. Biol. 329, 1-8.pdf
68. F. Dong, M. Vijayakumar, and H.-X. Zhou (2003). Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar. Biophys. J. 85, 49-60.pdf
67. H.-X. Zhou (2003). Direct test of the Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins. J. Am. Chem. Soc. 125, 2060-2061.pdf
66. H.-X. Zhou and F. Dong (2003). Electrostatic contributions to the stability of a thermophilic cold shock protein. Biophys. J. 84, 2216-2222.pdf
65. H.-X. Zhou (2003). Theory for the rate of contact formation in a polymer chain with local conformational transitions. J. Chem. Phys. 118, 2010-2015.pdf
2002
64. H.-X. Zhou (2002). Toward the physical basis of thermophilic proteins: linking of enriched polar interactions and reduced heat capacity of unfolding. Biophys. J. 83, 3126-3133.pdf
63. H.-X. Zhou (2002). Residual charge interactions in unfolded staphylococcal nuclease can be explained by the Gaussian-chain model. Biophys. J. 83, 2981-2986.pdf
62. F. Dong and H.-X. Zhou (2002). Electrostatic contributions to T4 lysozyme stability: solvent-exposed charges versus semi-buried salt bridges. Biophys. J. 83, 1341-1347.pdf
61. H.-X. Zhou (2002). Residual electrostatic effects in the unfolded state of the N-terminal domain of L9 can be attributed to non-specific non-local charge-charge interactions. Biochemistry 41, 6533-6538.pdf
60. H.-X. Zhou (2002). Dimensions of denatured proteins chains from hydrodynamic data. J. Phys. Chem. B 106, 5769-5775.pdf
59. H.-X. Zhou (2002). A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins. Proc. Natl. Acad. Sci. USA 99, 3569-3574.pdf Faculty of 1000 Evaluation
58. H.-X. Zhou and R. Zwanzig (2002). Barrier crossing coupled to a small set of oscillators. J. Phys. Chem. A 106, 7562-7564.pdf
57. A. H. Boschitsch, M. O. Fenley, and H.-X. Zhou (2002). Fast boundary element method for the linear Poisson-Boltzmann equation. J. Phys. Chem. B 202, 2741-2754.pdf
56. H.-X. Zhou (2002). A model for the binding of the inactivation N-terminal to the ion pore of Shaker potassium channel: both electrostatic attraction and covalent linkage are required for rapid inactivation. J. Phys. Chem. B 106, 2393-2397.pdf
2001
55. H.-X. Zhou (2001). The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteins. Biochemistry 40, 15069-15073.pdf Faculty of 1000 Evaluation
54. H.-X. Zhou and K. A. Dill (2001). Stabilization of proteins in confined spaces. Biochemistry 40, 11289-11293.pdf Faculty of 1000 Evaluation
53. M. Vijayakumar and H.-X. Zhou (2001). Salt bridges stabilize the folded structure of barnase. J. Phys. Chem. B 105, 7334-7340.pdf
52. H.-X. Zhou (2001). Single-chain versus dimeric protein folding: thermodynamic and kinetic consequences of covalent linkage. J. Am. Chem. Soc. 123, 6730-6731.pdf
51. H.-X. Zhou (2001). Loops in proteins can be modeled as worm-like chains. J. Phys. Chem. B 105, 6763-6766.pdf
50. H.-X. Zhou and Y. Shan (2001). Prediction of protein interaction sites from sequence profiles and residue neighbor list. Proteins 44, 336-343.pdf
49. H.-X. Zhou (2001). Disparate ionic-strength dependence of on and off rates in protein- protein association. Biopolymers 59, 427-433.pdf Faculty of 1000 Evaluation
48. H.-X. Zhou and G. Wang (2001). Predicted structures of two proteins involved in human diseases. Cell Biochem. Biophys. 35, 35-47.pdf
47. H.-X. Zhou (2001). A unified picture of protein hydration: prediction of hydrodynamic properties from known structures. Biophys. Chem. 93, 171-179.pdf
46. Y. Shan, G. Wang, and H.-X. Zhou (2001). Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading. Proteins 42, 23-37.pdf