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Zhou Group Publications


    235. H.-X. Zhou (2017). Gating motions and stationary gating properties of ionotropic glutamate receptors: computation meets electrophysiology. Acc. Chem. Res. (in press).pdf

    234. H.-X. Zhou and L. P. Wollmuth (2017). Advancing NMDA receptor physiology by integrating multiple approaches. Trends Neurosci. (in press).pdf

    233. X. Pang and H.-X. Zhou (2017). Rate constants and mechanisms of protein-ligand binding. Annu. Rev. Biophys. (in press).

    232. S. Qin and H.-X. Zhou (2017). Protein folding, binding, and droplet formation in cell-like conditions. Curr. Opin. Struct. Biol. 43, 28-37.pdf

    231. H.-X. Zhou (2017). Biophysics: past, present, and future. In Reference Module in Life Sciences: Elsevier.pdf


    230. C. Guo and H.-X. Zhou (2016). Unidirectional allostery in the regulatory subunit RIα facilitates efficient deactivation of protein kinase A. 113, E6776-E6785.pdf

    229. J. Guo and H.-X. Zhou (2016). Allosteric activation of SENP1 by SUMO1 β-grasp domain involves a dock-and-coalesce mechanism. eLife 5, e18249.pdf

    228. J. Dai and H.-X. Zhou (2016). Semiclosed conformations of the ligand-binding domains of NMDA receptors during stationary gating. Biophys. J. 111, 1418-1428..pdf

    227. S. Qin and H.-X. Zhou (2016). Fast method for computing chemical potentials and liquid-liquid phase equilibria of macromolecular solutions. J. Phys. Chem. B. 120, 8164-8174.pdf

    226. W. Im, J. Liang, A. Olson, H.-X. Zhou, S. Vajda, and I. A. Vakser (2016). Challenges in structural approaches to cell modeling. J. Mol. Biol. 28, 2943-2964.pdf

    225. J. Batra, H. Tjong, and H.-X. Zhou (2016). Electrostatic effects on the folding stability of FKBP12. Protein Eng. Des. Sel. 29, 301-308.pdf

    224. X. Pang and H.-X. Zhou (2016). Mechanism and rate constants of the Cdc42 GTPase binding with intrinsically disordered effectors. Proteins 84, 674-685.pdf

    223. J. Guo and H.-X. Zhou (2016). Protein allostery and conformational dynamics. Chem. Rev. 116, 6503-6515.pdf

    222. A. Wright, P. Batsomboon, J. Dai, I. Hung, H.-X. Zhou, G. Dudley, and T. A. Cross (2016). Differential binding of rimantadine enantiomers to Influenza A M2 proton channel. J. Am. Chem. Soc. 138, 1506-1509.pdf

    221. Q. Gan, J. Dai, H.-X. Zhou, and L. P. Wollmuth (2016). The transmembrane domain mediates tetramerization of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. J. Biol. Chem. 291, 6595-6606.pdf

    220. M. F. Lensink, S. Velankar, A. Kryshtafovych, S.-Y. Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N. Fernandez-Fuentes, S. Viswanath, R. Elber, S. Grudinin, P. Popov, E. Neveu, H. Lee, M. Baek, S. Park, L. Heo, G. R. Lee, C. Seok, S. Qin, H.-X. Zhou, D. W. Ritchie, B. Maigret, M.-D. Devignes, A. Ghoorah, M. Torchala, R. A. G. Chaleil, P. A. Bates, E. Ben-Zeev, M. Eisenstein, S. S. Negi, Z. Weng, T. Vreven, B. G. Pierce, T. M. Borrman, J. Yu, F. Ochsenbein, R. Guerois, A. Vangone, J. P. G. L. M. Rodrigues, G. van Zundert, M. Nellen, L. Xue, E. Karaca, A. S. J. Melquiond, K. Visscher, P. L. Kastritis, A. M. J. J. Bonvin, X. Xu, L. Qiu, C. Yan, J. Li, Z. Ma, J. Cheng, X. Zou, Y. Shen, L. X. Peterson, H.-R. Kim, A. Roy, X. Han, J. Esquivel-Rodriguez, D. Kihara, X. Yu, N. J. Bruce, J. C. Fuller, R. C. Wade, I. Anishchenko, P. J. Kundrotas, I. A. Vakser, K. Imai, K. Yamada, T. Oda, T. Nakamura, K. Tomii, C. Pallara, M. Romero-Durana, B. Jiménez-García, I. H. Moal, J. Férnandez-Recio, J. Y. Joung, J. Y. Kim, K. Joo, J. Lee, D. Kozakov, S. Vajda, S. Mottarella, D. R. Hall, D. Beglov, A. Mamonov, B. Xia, T. Bohnuud, C. A. Del Carpio, E. Ichiishi, N. Marze, D. Kuroda, S. S. Roy Burman, J. J. Gray, E. Chermak, L. Cavallo, R. Oliva, A. Tovchigrechko, and S. J. Wodak (2016). Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment. Proteins 84 (Suppl 1), 323-348.pdf


    219. Y. Miao, R. Fu, H.-X. Zhou, and T. A. Cross (2015). Dynamic short hydrogen bonds in histidine tetrad of full length M2 proton channel reveal tetrameric structural heterogeneity and functional mechanism. Structure 23, 2300-2308.pdf.

    218. X. Pang and H.-X. Zhou (2015). Disorder-to-order transition of an active-site loop mediates the allosteric activation of sortase A. Biophys. J. 109, 1706-1715.pdf

    217. J. Guo and H.-X. Zhou (2015). Dynamically driven protein allostery exhibits disparate responses for fast and slow motions. Biophys. J. 108, 2771-2774.pdf

    216. J. Dai, L. P. Wollmuth, and H.-X. Zhou (2015). Mechanism-based mathematical model for gating of ionotropic glutamate receptors. J. Phys. Chem. B 119, 10934-10940.pdf

    215. N. Das, J. Dai, I. Hung, M. Rajagopalan, H.-X. Zhou, and T. A. Cross (2015). Structure of CrgA, a cell division structural and regulatory protein from Mycobacterium tuberculosis, in lipid bilayers. Proc. Natl. Acad. Sci. USA 112, E119-E126.pdf  Faculty of 1000 Evaluation

    214. J. Dai and H.-X. Zhou (2015). Reduced curvature of ligand-binding domain free energy surface underlies partial agonism at NMDA receptors. Structure 23, 228-236.pdf

    213. J. Guo, X. Pang, and H.-X. Zhou (2015). Two pathways mediate inter-domain allosteric regulation in Pin1. Structure 23, 237-247.pdf


    212. A. M. Berezhkovskii, A. Szabo, N. Greives, and H.-X. Zhou (2014). Multidimensional reaction rate theory with anisotropic diffusion. J. Chem. Phys. 141, 204106.pdf

    211. J. Dai and H.-X. Zhou (2014). General rules for the arrangements and gating motions of pore-lining helices in homomeric ion channels. Nat. Commun. 5, 4641.pdf  Supplementary Information

    210. N. Greives and H.-X. Zhou (2014). Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit. Proc. Natl. Acad. Sci. USA 111, 10197-10202.pdf

    209. S. Qin and H.-X. Zhou (2014). Further development of the FFT-based method for atomistic modeling of protein folding and binding under crowding: optimization of accuracy and speed. J. Chem. Theory Comput. 10, 2824-2835.pdf.

    208. R. Kazi, J. Dai, C. Sweeney, H.-X. Zhou, and L. P. Wollmuth (2014). Mechanical coupling maintains the fidelity of NMDA receptor-mediated currents. Nat. Neurosci. 17, 914-922.pdf  Supplementary Information

    207. X. Pang and H.-X. Zhou (2014). Design rules for selective binding of nuclear localization signals to minor site of importin α. PLoS ONE 9, e91025.pdf

    206. H.-X. Zhou and O. Bilsel (2014). SAXS/SANS probe of intermolecular interactions in concentrated protein solutions. Biophys. J. 106, 771-773.pdf

    205. H.-X. Zhou (2014). Theoretical frameworks for multiscale modeling and simulation. Curr. Opin. Struct. Biol. 25, 67-76.pdf

    204. X. Pang and H.-X. Zhou (2014). Distinct mechanisms of a phosphotyrosyl peptide binding to two SH2 domains. J. Theor. Comput. Chem. 13, 1440003.pdf

    203. F. L. Jean-Francoisa, J. Dai, Y. Lue, A. Myrick, E. Rubin, P. G. Fajer, L. Song, H.-X. Zhou, and T. A. Cross (2014). Binding of MgtR, a Salmonella transmembrane regulatory peptide, to MgtC, a Mycobacterium tuberculosis virulence factor: a structural study. J. Mol. Biol. 426, 436-446.pdf

    202. M. F. Lensink, I. H. Moal, P. A. Bates, P. L. Kastritis, A. S. J. Melquiond, E. Karaca, C. Schmitz, M. van Dijk, A. M. J. J. Bonvin, M. Eisenstein, B. Jimenez-Garcia, S. Grosdidier, A. Solernou, L. Perez-Cano, C. Pallara, J. Fernendez-Recio, J. Xu, P. Muthu, K. P. Kilambi, J. J. Gray, S. Grudinin, G. Derevyanko, J. C. Mitchell, J. Wieting, E. Kanamori, Y. Tsuchiya, Y. Murakami, J. Sarmiento, D. M. Standley, M. Shirota, K. Kinoshita, H. Nakamura, M. Chavent, D. W. Ritchie, H. Park, J. Ko, H. Lee, C. Seok, Y. Shen, D. Kozakov, S. Vajda, P. J. Kundrotas, I. A. Vakser, B. G. Pierce, H. Hwang, T. Vreven, Z. Weng, I. Buch, E. Farkash, H. J. Wolfson, M. Zacharias, S. Qin, H.-X. Zhou, S.-Y. Huang, X. Zou, J. A. Wojdyla, C. Kleanthous, and S. J. Wodak (2014). Blind prediction of interfacial water positions in CAPRI. Proteins 82, 620-632.pdf


    201. S. Qin and H.-X. Zhou (2013). Effects of macromolecular crowding on the conformational ensembles of disordered proteins. J. Phys. Chem. Lett. 4, 3429-3434.pdf

    200. G. Heymann, J. Dai, M. Li, S. D. Silberberg, H.-X. Zhou, and K. J. Swartz (2013). Inter- and intrasubunit interactions between transmembrane helices in the open state of P2X receptor channels. Proc. Natl. Acad. Sci. USA 110, E4045-E4054.pdf

    199. A. R. Cormier, X. Pang, M. I. Zimmerman, H.-X. Zhou, and A. K. Paravastu (2013). Molecular structure of RADA16-I designer self-assembling peptide nanofibers. ACS Nano 7, 7562-7572.pdf

    198. S. Qin and H.-X. Zhou (2013). FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders. J. Chem. Theory Comput. 9, 4633-4643.pdf

    197. A. C. Miklos, M. Sumpter, and H.-X. Zhou (2013). Competitive interactions of ligands and macromolecular crowders with maltose binding protein. PLoS ONE 8, e74969.pdf

    196. S. Qin and H.-X. Zhou (2013). Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond. Proteins 81, 2229-2236.pdf

    195. R. Moretti, S. J. Fleishman, R. Agius, M. Torchala, P. A. Bates, P. L. Kastritis, J. P. G. L. M. Rodrigues, M. Trellet, A. M. J. J. Bonvin, M. Cui, M. Rooman, D. Gillis, Y. Dehouck, I. Moal, M. Romero-Durana, L. Perez-Cano, C. Pallara, B. Jimenez, J. Fernandez-Recio, S. Flores, M. Pacella, K. P. Kilambi, J. J. Gray, P. Popov, S. Grudinin, J. Esquivel-Rodríguez, D. Kihara, N. Zhao, D. Korkin, X. Zhu, O. N. A. Demerdash, J. C. Mitchell, E. Kanamori, Y. Tsuchiya, H. Nakamura, H. Lee, H. Park, C. Seok, J. Sarmiento, S. Liang, S. Teraguchi, D. M. Standley, H. Shimoyama, G. Terashi, M. Takeda-Shitaka, M. Iwadate, H. Umeyama, D. Beglov, D. R. Hall, D. Kozakov, S. Vajda, B. G. Pierce, H. Hwang, T. Vreven, Z. Weng, Y. Huang, H. Li, X. Yang, X. Ji, S. Liu, Y. Xiao, M. Zacharias, S. Qin, H.-X. Zhou, S.-Y. Huang, X. Zou, S. Velankar, J. Janin, S. J. Wodak, and D. Baker (2013). Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins 81, 1980-1987.pdf

    194. X. Pang and H.-X. Zhou (2013). Activation of signaling receptors: do ligands bind to receptor monomer, dimer, or both? BMC Biophys. 6, 7.pdf

    193. H.-X. Zhou and P. A. Bates (2013). Modeling protein association mechanisms and kinetics. Curr. Opin. Struct. Biol. 23, 887-893.pdf

    192. S. R. Leonard, A. R. Cormier, X. Pang, M. I. Zimmerman, H.-X. Zhou, and A. K. Paravastu (2013). Solid-state NMR evidence for β-hairpin structure within MAX8 designer peptide nanofibers. Biophys. J. 105, 222-230.pdf

    191. H. Dong, M. Yi, T.A. Cross, and H.-X. Zhou (2013). Ab initio calculations and validation of the pH-dependent structures of the His37-Trp41 quartet, the heart of acid activation and proton conductance in the M2 protein of Influenza A virus. Chem. Sci. 4, 2776-2787.pdf  Supplementary Material

    190. J. Dai and H.-X. Zhou (2013). An NMDA receptor gating mechanism developed from MD simulations reveals molecular details underlying subunit-specific contributions. Biophys. J. 104, 2170-2181.pdf

    189. H.-X. Zhou and T. A. Cross (2013). Modeling the membrane environment has implications for membrane protein structure and function: Influenza A M2 protein. Protein Sci. 22, 381-394.pdf

    188. H.-X. Zhou (2013). Influences of crowded cellular environments on protein folding, binding, and oligomerization: biological consequences and potentials of atomistic modeling. FEBS. Lett. 587, 1053-1061.pdf

    187. S. Qin, J. Mittal, and H.-X. Zhou (2013). Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation. Phys. Biol. 10, 045001.pdf  Phys. Biol. Highlights

    186. H.-X. Zhou (2013). Polymer crowders and protein crowders act similarly on protein folding stability. FEBS. Lett. 587, 394-397.pdf

    185. H.-X. Zhou and S. Qin (2013). Simulation and modeling of crowding effects on the thermodynamic and kinetic properties of proteins with atomic details. Biophys. Rev. 5, 207-215.pdf

    184. H.-X. Zhou and T. A. Cross (2013). Influences of membrane mimetic environments on membrane protein structures. Annu. Rev. Biophys. 42, 361-392.pdf  Supplemental Material

    183. S. Qin and H.-X. Zhou (2013). PI2PE: a suite of web servers for predictions ranging from protein structure to binding kinetics. Biophys. Rev. 5, 41-46.pdf

    182. X. Pang and H.-X. Zhou (2013). Poisson-Boltzmann calculations: van der Waals or molecular surface? Commun. Comput. Phys. 13, 1-12.pdf


    181. S. Qin, L. Cai, and H.-X. Zhou (2012). A method for computing association rate constants of atomistically represented proteins under macromolecular crowding. Phys. Biol. 9, 066008.pdf  Phys. Biol. Highlights

    180. N. Greives and H.-X. Zhou (2012). BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from Brownian dynamics simulations. J. Chem. Phys. 137, 135105.pdf

    179. C. K. P. Long, H.-X. Zhou, and P. B. Chase (2012). Familial hypertrophic cardiomyopathy related E180G mutation increases flexibility of human cardiac α-tropomyosin. FEBS Lett. 586, 3503-3507.pdf

    178. Y. Phillip, M. Harel, R. Khait, S. Qin, H.-X. Zhou, and G. Schreiber (2012). Contrasting factors on the kinetic path to protein complex formation diminish the effects of crowding agents. Biophys. J. 103, 1011-1019.pdf

    177. X. Pang, K. H. Zhou, S. Qin, and H.-X. Zhou (2012). Prediction and dissection of widely-varying association rate constants of actin-binding proteins. PLoS Comput. Biol. 8, e1002696.pdf

    176. H.-X. Zhou, X. Pang, and L. Cai (2012). Rate constants and mechanisms of intrinsically disordered proteins binding to structured targets. Phys. Chem. Chem. Phys. 14, 10466-10476.pdf  Faculty of 1000 Evaluation

    175. J. Du, T. A. Cross, and H.-X. Zhou (2012). Recent progress in structure-based anti-influenza drug design. Drug Discov. Today 17, 1111-1120.pdf

    174. J. Du, H. Dong, and H.-X. Zhou (2012). Size matters in activation/inhibition of ligand-gated ion channels. Trends Pharmacol. Sci. 33, 482-493.pdf

    173. C. K. P. Long, H.-X. Zhou, and P. B. Chase (2012). Persistence length of human cardiac α-tropomyosin measured by single molecule direct probe microscopy. PLoS ONE 7, e39676.pdf

    172. H. Dong, M. Sharma, H.-X. Zhou, and T. A. Cross (2012). Glycines: role in α-helical membrane protein structures and a potential indicator for native conformation. Biochemistry 51, 4779-4789.pdf  Supporting Information

    171. J. Du, H. Dong, and H.-X. Zhou (2012). Gating mechanism of a P2X4 receptor developed from normal mode analysis and molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 109, 4140-4145.pdf

    170. X. Pang and H.-X. Zhou (2012). A common model for cytokine receptor activation: combined scissor-like rotation and self-rotation of receptor dimer induced by class I cytokine. PLoS Comput. Biol. 8, e1002427.pdf

    169. T. A. Cross, H. Dong, M. Sharma, D. D. Busath, and H.-X. Zhou (2012). M2 protein from influenza A: from multiple structures to biophysical and functional insights. Curr. Opin. Virol. 2, 128-133.pdf

    168. A. Szabo and H.-X. Zhou (2012). Role of diffusion in the kinetics of reversible enzyme-catalyzed reactions. Bull. Korean Chem. Soc. 33, 925-928.pdf

    167. H.-X. Zhou (2012). Intrinsic disorder: signaling via highly specific but short-lived association. Trends Biochem. Sci. 37, 43-48.pdf


    166. S. Qin, X. Pang, and H.-X. Zhou (2011). Automated prediction of protein association rate constants. Structure 19, 1744-1751.pdf  Supplementary Information

    165. H.-X. Zhou (2011). Mechanistic insight into the H2O/D2O isotope effect in the proton transport of the influenza virus M2 protein. J. Membr. Biol. 244:93-96.pdf

    164. J. L. Barreda and H.-X. Zhou (2011). Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites. J. Chem. Phys. 135, 145101.pdf  JCP

    163. S. J. Fleishman, T. A. Whitehead, E.-M. Strauch, J. E. Corn, S. Qin, H.-X. Zhou, J. C. Mitchell, O. N. Demerdash, M. Takeda-Shitaka, G. Terashi, I. H. Moal, X. Li, P. A. Bates, M. Zacharias, H. Park, J. Ko, H. Lee, C. Seok, T. Bourquard, J. Bernauer, A. Poupon, J. Aze, S. Soner, S. K. Ovali, P. Ozbek, N. Ben Tal, T. Haliloglu, H. Hwang, T. Vreven, B. G. Pierce, Z. Weng, L. Perez-Cano, C. Pons, J. Fernadez-Recio, F. Jiang, F. Yang, X. Gong, L. Cao, X. Xu, B. Liu, P. Wang, C. Li, C. Wang, C. H. Robert, M. Guharoy, S. Liu, Y. Huang, L. Li , D. Guo, Y. Chen, Y. Xiao, N. London, Z. Itzhaki, O. Schueler-Furman, Y. Inbar, V. Patapov, M. Cohen, G. Schreiber, Y. Tsuchiya, E. Kanamori, D. M. Standley, H. Nakamura, K. Kinoshita, C. M. Driggers, R. G. Hall, J. L. Morgan, V. L. Hsu, J. Zhan, Y. Yang, Y. Zhou, P. L. Kastritis, A. M. J. J. Bonvin, W. Zhang, C. J. Camacho, K. P. Kilambi, A. Sircar, J. J. Gray, M, Ohue, N. Uchikoga, Y. Matsuzaki, T. Ishida, Y. Akiyama, R. Khashan, S. Bush, D. Fouches, A. Tropsha, J. Esquivel-Rodrigez, D. Kihara, P. B. Stranges, R. Jacak, B. Kuhlman, S. Huang, X. Zou, S. J. Wodak, J. Janin, and D. Baker (2011). Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J. Mol. Biol. 414, 289-302.pdf

    162. A. M. Berezhkovskii, A. Szabo, and H.-X. Zhou (2011). Diffusion-influenced ligand binding to buried sites in macromolecules and transmembrane channels. J. Chem. Phys. 135, 075103.pdf

    161. X. Pang, S. Qin, and H.-X. Zhou (2011). Rationalizing 5,000-fold differences in receptor-binding rate constants of four cytokines. Biophys. J. 101, 1175-1183.pdf

    160. H. Dong and H.-X. Zhou (2011). Atomistic mechanism for the activation and desensitization of an AMPA-subtype glutamate receptor. Nat. Commun. 2, 354.pdf

    159. H.-X. Zhou (2011). Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteins. Proc. Natl. Acad. Sci. USA. 108, 8651-8656.pdf  Supporting Text  Faculty of 1000 Evaluation

    158. H.-X. Zhou (2011). Equivalence of two approaches for modeling ion permeation through a transmembrane channel with an internal binding site. J. Chem. Phys. 134, 135101.pdf  JCP

    157. H.-X. Zhou (2011). Q&A: What is biophysics? BMC Biology 9, 13.pdf

    156. J. L. Barreda and H.-X. Zhou (2011). A solvable model for the diffusion and reaction of neurotransmitters in a synaptic junction. BMC Biophys. 4, 5.pdf

    155. L. Cai and H.-X. Zhou (2011). Theory and simulation on the kinetics of protein-ligand binding coupled to conformational change. J. Chem. Phys. 134, 105101.pdf

    154. H.-X. Zhou (2011). A theory for the proton transport of the influenza virus M2 protein: extensive test against conductance data. Biophys. J. 100, 912-921.pdf

    153. S. Qin and H.-X. Zhou (2011). Structural models of protein-DNA complexes based on interface prediction and docking. Curr. Protein Pept. Sci. 12, 531-539.pdf

    152. T. A. Cross, M. Sharma, M. Yi, and H.-X. Zhou (2011). Influence of solubilizing environments on membrane protein structures. Trends Biochem. Sci. 36, 117-125.pdf

    151. M. Sharma, C. Li, D. D Busath, H.-X. Zhou, and T. A. Cross (2011). Drug sensitivity, drug-resistant mutations, and structures of the conductance domains of three viral porins. BBA-Biomembranes 1808, 538-546.pdf


    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


    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


    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


    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.

    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


    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


    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


    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.


    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.reprint

    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


    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


    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


    45. M. Vijayakumar and H.-X. Zhou (2000). Prediction of residue-residue pair frequencies in proteins. J. Phys. Chem. B 104, 9755-9764.pdf

    44. Y. Shan and H.-X. Zhou (2000). Correspondence of potentials of mean force in proteins and in liquids. J. Chem. Phys. 113, 4794-4798.pdf

    43. A. M. Berezhkovskii, A. Szabo, G. H. Weiss, and H.-X. Zhou (1999). Reaction dynamics on a thermally fluctuating potential. J. Chem. Phys. 111, 9952-9957.

    42. M. Vijayakumar, H. Qian, and H.-X. Zhou (1999). Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities. Proteins 34, 497-507.

    41. H.-X. Zhou, S. T. Wlodek, and J. A. McCammon (1998). Conformation gating as a mechanism for enzyme specificity. Proc. Natl. Acad. Sci. USA 95, 9280-9283.pdf

    40. M. Vijayakumar, K.-Y. Wong, G. Schreiber, A. R. Fersht, A. Szabo, and H.-X. Zhou (1998). Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar. J. Mol. Biol. 278, 1015-1024.pdf

    39. H.-X. Zhou (1998). Theory of the diffusion-influenced substrate binding rate to a buried and gated active site. J. Chem. Phys.108, 8146-8154.

    38. H.-X. Zhou (1998). Comparison of three Brownian-dynamics algorithms for calculating rate constants of diffusion-influenced reactions. J. Chem. Phys.108, 8139-8145.

    37. H.-X. Zhou, J. M. Briggs, S. Tara, and J. A. McCammon (1998). Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site. Biopolymers 45, 355-360.

    36. H.-X. Zhou (1997). Enhancement of protein-protein association rate by interaction potential: accuracy of prediction based on local Boltzmann factor. Biophys. J. 73, 2441-2445.

    35. H.-X. Zhou, K.-Y. Wong, and M. Vijayakumar (1997). Design of fast enzymes by optimizing interaction potential in active site. Proc. Natl. Acad. Sci. USA 94, 12372-12377.

    34. H.-X. Zhou (1997). Theory and simulation of the influence of diffusion in enzyme-catalyzed reactions. J. Phys. Chem. B 101, 6642-6651.

    33. H.-X. Zhou and M. Vijayakumar (1997). Modeling of protein conformational fluctuations in pKa predictions. J. Mol. Biol. 267, 1002-1011.

    32. H.-X. Zhou (1997). Control of reduction potential by protein matrix: lesson from a spherical protein model. J. Biol. Inorg. Chem. 2, 109-113.

    31. H.-X. Zhou, J. M. Briggs, and J. A. McCammon (1996). A 240-fold electrostatic rate-enhancement for acetylcholinesterase-substrate binding can be predicted by the potential within the active site. J. Am. Chem. Soc. 118, 13069-13070.

    30. H.-X. Zhou (1996). Effect of interaction potentials in diffusion-influenced reactions with small reactive regions. J. Chem. Phys. 105, 7235-7237.

    29. H.-X. Zhou and A. Szabo (1996). Theory and simulation of the time-dependent rate coefficients of diffusion-influenced reactions. Biophys. J. 71, 2440-2457.

    28. H.-X. Zhou (1996). Dielectric continuum model for calculating reorganization free energies of electron transfer in proteins. J. Chem. Phys. 105, 3726-3733.

    27. H.-X. Zhou and Y. Chen (1996). Chemically driven motility of Brownian particles. Phys. Rev. Lett. 77, 194-197.

    26. M. J. Potter, B. Luty, H.-X. Zhou, and J. A. McCammon (1996). Time-dependent rate coefficients from Brownian dynamics simulations. J. Phys. Chem. 100, 5149-5154.

    25. H.-X. Zhou and A. Szabo (1996). Theory and simulation of stochastically-gated diffusion-influenced reactions. J. Phys. Chem. 100, 2597-2604.

    24. J. A. Ernst, R. T. Clubb, H.-X. Zhou, A. M. Gronenborn, and G. M. Clore (1995). Use of NMR to detect water within nonpolar protein cavities. Science 270, 1848-1849.

    23. H.-X. Zhou (1995). Calculation of translational friction and intrinsic viscosity. II. Application to globular proteins. Biophys. J. 69, 2298-2303.

    22. H.-X. Zhou (1995). Calculation of translational friction and intrinsic viscosity. I. General formulation for arbitrarily shaped particles. Biophys. J. 69, 2286-2297.

    21. H.-X. Zhou and A. Szabo (1995). Microscopic formulation of Marcus' theory of electron transfer. J. Chem. Phys. 103, 3481-3494.

    20. J. A. Ernst, R. T. Clubb, H.-X. Zhou, A. M. Gronenborn, and G. M. Clore (1995). Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science 267, 1813-1817.

    19. H.-X. Zhou (1995). Continuum-model studies of redox reactions, complex formation, and electron transfer: the paradigm of cytochrome c and cytochrome c peroxidase. in A. Pullman, J. Jortner, and B. Pullman (Eds.), "Modelling of Biomolecular Structures and Mechanisms", 381-398. Kluwer Academic Publishers, Dordrecht.

    18. H.-X. Zhou (1994). Effects of mutations and complex formation on the redox potentials of cytochrome c and cytochrome c peroxidase. J. Am. Chem. Soc. 116, 10362-10375.

    17. J. F. Douglas, H.-X. Zhou, and J. B. Hubbard (1994). Hydrodynamic friction and the electrostatic capacitance of an arbitrarily-shaped objects. Phys. Rev. E 49, 5319-5331.

    16. H.-X. Zhou, A. Szabo, J. F. Douglas, and J. B. Hubbard (1994). A Brownian dynamics algorithm for calculating the hydrodynamic friction and the electrostatic capacitance of an arbitrarily-shaped object. J. Chem. Phys. 100, 3821-3826.

    15. H.-X. Zhou (1994). Macromolecular electrostatic energy within the nonlinear Poisson-Boltzmann equation. J. Chem. Phys. 100, 3152-3162.

    14. O. Schaad, H.-X. Zhou, A. Szabo, W. A. Eaton, and E. R. Henry (1993). Simulation of the kinetics of ligand binding to a protein by molecular dynamics: geminate rebinding of nitric oxide to myoglobin. Proc. Natl. Acad. Sci. USA 90, 9547-9551.

    13. H.-X. Zhou (1993). Boundary element solution of macromolecular electrostatics: interaction energy between two proteins. Biophys. J. 65, 955-963.

    12. H.-X. Zhou (1993). Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein-protein association kinetics. Biophys. J. 64, 1711-1726.

    11. H.-X. Zhou (1993). Dynamic spherical model for solvation in a dipolar lattice. J. Phys. Chem. 97, 4216-4223.

    10. H.-X. Zhou, B. Bagchi, A. Papazyan, and M. Maroncelli (1992). Solvation dynamics in a Brownian dipole lattice: a comparison between theory and computer simulation. J. Chem. Phys. 97, 9311-9320.

    9. B. A. Luty, J. A. McCammon, and H.-X. Zhou (1992). Diffusive reaction rates from Brownian dynamics simulations: replacing the outer cut-off surface by an analytical treatment. J. Chem. Phys. 97, 5682-5686.

    8. H.-X. Zhou and B. Bagchi (1992). Dielectric and orientational relaxation in a Brownian dipolar lattice. J. Chem. Phys. 97, 3610-3620.

    7. H.-X. Zhou and A. Szabo (1991). Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard sphere liquid. J. Chem. Phys. 95, 5948-5952.

    6. H.-X. Zhou and R. Zwanzig (1991). A rate process with an entropy barrier. J. Chem. Phys. 94, 6147-6152.

    5. H.-X. Zhou (1990). Kinetics of diffusion-influenced reactions studied by Brownian dynamics. J. Phys. Chem. 94, 8794-8800.

    4. H.-X. Zhou and F. A. Ferrone (1990). Theoretical description of the spatial dependence of sickle hemoglobin polymerization. Biophys. J. 58, 695-703.

    3. H.-X. Zhou and A. Szabo (1990). Mean field theory of transient fluorescence quenching in the frequency domain. J. Chem. Phys. 92, 3874-3880.

    2. H.-X. Zhou (1990). On the calculation of diffusive reaction rates using Brownian dynamics simulations. J. Chem. Phys. 92, 3092-3095.

    1. H.-X. Zhou (1989). The exponential nature of barrier crossings studied by Langevin dynamics. Chem. Phys. Lett. 164, 285-290.