2013

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