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Regis Pomes, Ph.D. - Publications

Affiliations: 
1988 Ecole Supérieure de Chimie Industrielle de Lyon, France 
 1993 chemistry University of Houston, Houston, TX, United States 
 1993-1996 Physics Université de Montréal, Montréal, Canada 
 2000- Biochemistry University of Toronto, Toronto, ON, Canada 
 2000- Structural Biology and Biochemistry Hospital for Sick Children, Toronto, ON 
Area:
biophysics, membrane transport, statistical thermodynamics, computer simulation
Website:
http://local.biochemistry.utoronto.ca/pomes/
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Year Citation  Score
2020 Zhou S, Pettersson P, Huang J, Brzezinski P, Pomès R, Mäler L, Ädelroth P. NMR Structure and Dynamics Studies of Yeast Respiratory Supercomplex Factor 2. Structure (London, England : 1993). PMID 32905793 DOI: 10.1016/J.Str.2020.08.008  0.396
2020 Yamashita M, Ing CE, Yeung PS, Maneshi MM, Pomès R, Prakriya M. The basic residues in the Orai1 channel inner pore promote opening of the outer hydrophobic gate. The Journal of General Physiology. 152. PMID 31816637 DOI: 10.1085/Jgp.201912397  0.333
2020 Hossain L, Srivastava A, Huynh Q, Pomès R. Uncovering the Structural Basis for the Mechanical Properties of Elastin Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2939  0.302
2020 Huang J, Pomès R. A Molecular Simulation Method to Predict the Solvation, Fold, Self-Assembly, and Poration of Peptides and Proteins in Membranes Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2230  0.405
2019 Banh R, Cherny VV, Morgan D, Musset B, Thomas S, Kulleperuma K, Smith SME, Pomès R, DeCoursey TE. Hydrophobic gasket mutation produces gating pore currents in closed human voltage-gated proton channels. Proceedings of the National Academy of Sciences of the United States of America. PMID 31462498 DOI: 10.1073/Pnas.1905462116  0.309
2019 Zeng ZW, Ing C, Pomès R. Molecular Dynamics Study of the Gating Mechanism of CFTR Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.1891  0.313
2019 Srivastava A, Xue Z, Muiznieks LD, Keeley FW, Pomes R. Solvent Effects on the Self-Assembly and Mechanical Properties of Elastin-Like Peptides Biophysical Journal. 116: 202a. DOI: 10.1016/J.Bpj.2018.11.1115  0.353
2018 Muiznieks LD, Sharpe S, Pomès R, Keeley FW. Role of Liquid-Liquid Phase Separation in Assembly of Elastin and Other Extracellular Matrix Proteins. Journal of Molecular Biology. PMID 29886015 DOI: 10.1016/J.Jmb.2018.06.010  0.347
2018 Jiang D, Gamal El-Din TM, Ing C, Lu P, Pomès R, Zheng N, Catterall WA. Structural basis for gating pore current in periodic paralysis. Nature. PMID 29769724 DOI: 10.1038/S41586-018-0120-4  0.306
2018 Yeung PS, Yamashita M, Ing CE, Pomès R, Freymann DM, Prakriya M. Mapping the functional anatomy of Orai1 transmembrane domains for CRAC channel gating. Proceedings of the National Academy of Sciences of the United States of America. PMID 29760086 DOI: 10.1073/Pnas.1718373115  0.346
2018 Ye L, Neale C, Sljoka A, Lyda B, Pichugin D, Tsuchimura N, Larda ST, Pomès R, García AE, Ernst OP, Sunahara RK, Prosser RS. Mechanistic insights into allosteric regulation of the A adenosine G protein-coupled receptor by physiological cations. Nature Communications. 9: 1372. PMID 29636462 DOI: 10.1038/S41467-018-03314-9  0.345
2018 Zhou S, Pettersson P, Huang J, Sjöholm J, Sjöstrand D, Pomès R, Högbom M, Brzezinski P, Mäler L, Ädelroth P. Solution NMR structure of yeast Rcf1, a protein involved in respiratory supercomplex formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 29507228 DOI: 10.1073/Pnas.1712061115  0.41
2018 Rauscher S, Pomès R. The Liquid-Like Structure of Elastin Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.2043  0.657
2017 Rauscher S, Pomès R. The liquid structure of elastin. Elife. 6. PMID 29120326 DOI: 10.7554/Elife.26526  0.732
2017 Wang H, Muiznieks LD, Ghosh P, Williams D, Solarski M, Fang A, Ruiz-Riquelme A, Pomès R, Watts JC, Chakrabartty A, Wille H, Sharpe S, Schmitt-Ulms G. Somatostatin binds to the human amyloid β peptide and favors the formation of distinct oligomers. Elife. 6. PMID 28650319 DOI: 10.7554/Elife.28401  0.341
2017 Lenaeus MJ, Gamal El-Din TM, Ing C, Ramanadane K, Pomès R, Zheng N, Catterall WA. Structures of closed and open states of a voltage-gated sodium channel. Proceedings of the National Academy of Sciences of the United States of America. PMID 28348242 DOI: 10.1073/Pnas.1700761114  0.359
2017 Kim TH, Mehrabi P, Ren Z, Sljoka A, Ing C, Bezginov A, Ye L, Pomès R, Prosser RS, Pai EF. The role of dimer asymmetry and protomer dynamics in enzyme catalysis. Science (New York, N.Y.). 355. PMID 28104837 DOI: 10.1126/Science.Aag2355  0.347
2017 Wang H, Muiznieks LD, Ghosh P, Williams D, Solarski M, Fang A, Ruiz-Riquelme A, Pomès R, Watts JC, Chakrabartty A, Wille H, Sharpe S, Schmitt-Ulms G. Author response: Somatostatin binds to the human amyloid β peptide and favors the formation of distinct oligomers Elife. DOI: 10.7554/Elife.28401.022  0.337
2017 Rauscher S, Pomès R. Author response: The liquid structure of elastin Elife. DOI: 10.7554/Elife.26526.028  0.647
2017 Ing C, Chakrabarti N, Zheng N, Catterall WA, Pomès R. Role of Channel Fluctuations in Ion Transport and Selectivity in Bacterial Sodium Channel NavAb Biophysical Journal. 112: 105a. DOI: 10.1016/J.Bpj.2016.11.598  0.355
2017 Neale C, Pomès R, Sterne-Marr R, García A. Protein Folding upon Binding Revealed by Molecular Dynamics Simulation Biophysical Journal. 112: 54a. DOI: 10.1016/J.Bpj.2016.11.329  0.345
2017 Muiznieks LD, Keeley FW, Pomès R. Controlling the Biophysical Properties and Functionality of Phase-Separated Elastin-Based Droplets through Amino Acid Sequence Mutations Biophysical Journal. 112: 480a-481a. DOI: 10.1016/J.Bpj.2016.11.2601  0.321
2017 Huang J, Pomes R. A Molecular Simulation Method to Predict the Self-Assembly of Helix Bundles in Biological Membranes Biophysical Journal. 112: 359a. DOI: 10.1016/J.Bpj.2016.11.1949  0.337
2017 Huynh Q, Reichheld S, Rauscher S, Hao Wu Z, Sharpe S, Pomès R. Structure and Self-Assembly of Elastin-Like Peptides: A Joint Molecular Dynamics and NMR Study Biophysical Journal. 112: 206a-207a. DOI: 10.1016/J.Bpj.2016.11.1142  0.741
2016 Vallurupalli P, Chakrabarti N, Pomès R, Kay LE. Atomistic picture of conformational exchange in a T4 lysozyme cavity mutant: an experiment-guided molecular dynamics study. Chemical Science. 7: 3602-3613. PMID 30008994 DOI: 10.1039/C5Sc03886C  0.394
2016 Ing C, Pomès R. Simulation Studies of Ion Permeation and Selectivity in Voltage-Gated Sodium Channels. Current Topics in Membranes. 78: 215-260. PMID 27586286 DOI: 10.1016/Bs.Ctm.2016.07.005  0.339
2016 Wang S, Ing C, Emami S, Jiang Y, Liang H, Pomès R, Brown LS, Ladizhansky V. Structure and Dynamics of Extracellular Loops in Human Aquaporin-1 from Solid-State NMR and Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 27583975 DOI: 10.1021/Acs.Jpcb.6B06731  0.41
2016 Xiong ZJ, Huang J, Poda G, Pomès R, Privé GG. Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis. Journal of Molecular Biology. 428: 3026-42. PMID 27349982 DOI: 10.1016/J.Jmb.2016.06.012  0.329
2016 Chan SW, Yau J, Ing C, Liu K, Farber P, Won A, Bhandari V, Kara-Yacoubian N, Seraphim TV, Chakrabarti N, Kay LE, Yip CM, Pomès R, Sharpe S, Houry WA. Mechanism of Amyloidogenesis of a Bacterial AAA+ Chaperone. Structure (London, England : 1993). PMID 27265850 DOI: 10.1016/J.Str.2016.05.002  0.378
2016 Neale C, Pomès R. Sampling errors in free energy simulations of small molecules in lipid bilayers. Biochimica Et Biophysica Acta. PMID 26952019 DOI: 10.1016/J.Bbamem.2016.03.006  0.324
2016 Neale C, Pomès R, García AE. Peptide Bond Isomerization in High-Temperature Simulations. Journal of Chemical Theory and Computation. 12: 1989-99. PMID 26866899 DOI: 10.1021/Acs.Jctc.5B01022  0.341
2015 Neale C, Herce HD, Pomès R, García AE. Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor? Biophysical Journal. 109: 1652-62. PMID 26488656 DOI: 10.1016/J.Bpj.2015.08.028  0.327
2015 Calmettes C, Ing C, Buckwalter CM, El Bakkouri M, Chieh-Lin Lai C, Pogoutse A, Gray-Owen SD, Pomès R, Moraes TF. The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD. Nature Communications. 6: 7996. PMID 26282243 DOI: 10.1038/Ncomms8996  0.308
2015 Neale C, Chakrabarti N, Pomorski P, Pai EF, Pomès R. Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA. Plos Computational Biology. 11: e1004303. PMID 26181442 DOI: 10.1371/Journal.Pcbi.1004303  0.348
2015 Ing C, Chakrabarti N, Zheng N, Catterall WA, Pomès R. Coupling of Channel Fluctuations in Ion Permeation and Selectivity in Bacterial Sodium Channel NavAb Biophysical Journal. 108: 575a. DOI: 10.1016/J.Bpj.2014.11.3144  0.366
2015 Huynh LK, Neale C, Pomès R, Chan HS. Global Contacts Direct Hydophobic Collapse in Protein Folding Biophysical Journal. 108: 515a. DOI: 10.1016/J.Bpj.2014.11.2825  0.412
2015 Kulleperuma K, Smith SM, DeCoursey TE, Pomes R. Free Energy Simulations of Ion Translocation through Voltage-Gated Proton Channel Hv1 Biophysical Journal. 108: 439a. DOI: 10.1016/J.Bpj.2014.11.2399  0.357
2014 Naqvi MA, Rauscher S, Pomès R, Rousseau D. The conformational ensemble of the β-casein phosphopeptide reveals two independent intrinsically disordered segments. Biochemistry. 53: 6402-8. PMID 25227946 DOI: 10.1021/Bi500107U  0.721
2014 Neale C, Hsu JC, Yip CM, Pomès R. Indolicidin binding induces thinning of a lipid bilayer. Biophysical Journal. 106: L29-31. PMID 24739184 DOI: 10.1016/J.Bpj.2014.02.031  0.396
2014 Ing C, Chakrabarti N, Payandeh J, Zheng N, Catterall WA, Pomès R. Catalysis and Selectivity of Na+ Permeation in Bacterial Sodium Channel NaVAb Biophysical Journal. 106: 131a. DOI: 10.1016/J.Bpj.2013.11.772  0.313
2014 Naqvi MA, Rauscher S, Pomès R, Rousseau D. The Structure of the β-Casein Phosphopeptide Consists of Two Independent Intrinsically Disordered Domains Biophysical Journal. 106: 484a. DOI: 10.1016/J.Bpj.2013.11.2732  0.715
2014 Pomès R. The Liquid State of (Elastomeric) Proteins Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.269  0.44
2014 kulleperuma k, Morgan D, Musset B, Smith SM, Rajan S, Cherny VV, DeCoursey TE, Pomes R. Molecular Dynamics Studies of Ion Permeation in Human Voltage-Gated Proton Channel Biophysical Journal. 106: 433a-434a. DOI: 10.1016/J.Bpj.2013.11.2439  0.367
2013 Neale C, Madill C, Rauscher S, Pomès R. Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal. Journal of Chemical Theory and Computation. 9: 3686-703. PMID 26584121 DOI: 10.1021/Ct301005B  0.692
2013 Chakrabarti N, Ing C, Payandeh J, Zheng N, Catterall WA, Pomès R. Catalysis of Na+ permeation in the bacterial sodium channel Na(V)Ab. Proceedings of the National Academy of Sciences of the United States of America. 110: 11331-6. PMID 23803856 DOI: 10.1073/Pnas.1309452110  0.323
2013 Li G, Pomès R. Binding mechanism of inositol stereoisomers to monomers and aggregates of Aβ(16-22). The Journal of Physical Chemistry. B. 117: 6603-13. PMID 23627280 DOI: 10.1021/Jp311350R  0.353
2013 Neale C, Ghanei H, Holyoake J, Bishop RE, Privé GG, Pomès R. Detergent-mediated protein aggregation. Chemistry and Physics of Lipids. 169: 72-84. PMID 23466535 DOI: 10.1016/J.Chemphyslip.2013.02.005  0.406
2013 Neale C, Madill C, Rauscher S, Pomès R. Acurately Quantifying Correlation Times that Exceed the Timescale of Molecular Dynamics Simulations Biophysical Journal. 104: 31a. DOI: 10.1016/J.Bpj.2012.11.207  0.703
2013 Gradinaru C, Mazouchi A, Rauscher S, Pomes R, Forman-Kay J. The Intrinsically Unstable SH3-DRKN Protein: Compactness, Conformations and Speed Biophysical Journal. 104: 190a-191a. DOI: 10.1016/J.Bpj.2012.11.1074  0.695
2012 Pfoh R, Li A, Chakrabarti N, Payandeh J, Pomès R, Pai EF. Structural asymmetry in the magnesium channel CorA points to sequential allosteric regulation. Proceedings of the National Academy of Sciences of the United States of America. 109: 18809-14. PMID 23112165 DOI: 10.1073/Pnas.1209018109  0.326
2012 Seo M, Rauscher S, Pomès R, Tieleman DP. Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides. Journal of Chemical Theory and Computation. 8: 1774-1785. PMID 22582033 DOI: 10.1021/Ct200876V  0.717
2012 Rauscher S, Pomès R. Structural disorder and protein elasticity. Advances in Experimental Medicine and Biology. 725: 159-83. PMID 22399324 DOI: 10.1007/978-1-4614-0659-4_10  0.682
2012 Popovic K, Holyoake J, Pomès R, Privé GG. Structure of saposin A lipoprotein discs. Proceedings of the National Academy of Sciences of the United States of America. 109: 2908-12. PMID 22308394 DOI: 10.1073/Pnas.1115743109  0.35
2012 Li G, Rauscher S, Baud S, Pomès R. Binding of inositol stereoisomers to model amyloidogenic peptides. The Journal of Physical Chemistry. B. 116: 1111-9. PMID 22091989 DOI: 10.1021/Jp208567N  0.713
2012 Seo M, Rauscher S, Pomès R, Tieleman DP. Deriving Transferable Parameters for the Coarse-Grained Martini Model: Application to Amyloid-Like and Elastin-Like Peptides Biophysical Journal. 102: 732a. DOI: 10.1016/J.Bpj.2011.11.3973  0.702
2012 Xue Z, Rauscher S, Pomès R. Solvent Effects on the Conformational Equilibrium of Elastin-Like and Amyloidogenic Peptides Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.3435  0.722
2012 Rauscher S, Pomès R. Aggregated yet Disordered: A Molecular Simulation Study of the Self-Aggregation of Elastin Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.247  0.727
2012 Neale C, Pomès R. Accelerating the Rate of Convergence of Umbrella Sampling Simulations in Lipid Bilayers Biophysical Journal. 102: 396a. DOI: 10.1016/J.Bpj.2011.11.2163  0.359
2012 Kulleperuma K, Smith SM, Holyoake J, Chakrabarti N, Morgan D, Musset B, DeCoursey TE, Cherny VV, Pomès R. A Homology Modeling-Simulation Protocol for Construction and Assessment of Hv1 Models Biophysical Journal. 102: 266a. DOI: 10.1016/J.Bpj.2011.11.1462  0.358
2012 Huynh LK, Nikolic A, Pomès R. Computational Study of Self-Aggregation and Interaction of Amyloidgenic Peptide Oligomers with a Lipid Bilayer Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.1330  0.446
2011 Neale C, Bennett WF, Tieleman DP, Pomès R. Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers. Journal of Chemical Theory and Computation. 7: 4175-88. PMID 26598360 DOI: 10.1021/Ct200316W  0.41
2011 Patel N, Dubins DN, Pomès R, Chalikian TV. Parsing partial molar volumes of small molecules: a molecular dynamics study. The Journal of Physical Chemistry. B. 115: 4856-62. PMID 21466176 DOI: 10.1021/Jp2012792  0.334
2011 Nikolic A, Baud S, Rauscher S, Pomès R. Molecular mechanism of β-sheet self-organization at water-hydrophobic interfaces. Proteins. 79: 1-22. PMID 20938982 DOI: 10.1002/Prot.22854  0.731
2011 Fadda E, Pomès R. On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics. Nucleic Acids Research. 39: 767-80. PMID 20876689 DOI: 10.1093/Nar/Gkq812  0.548
2011 Neale C, Chakrabarti N, Pai EF, Pomès R. Microsecond Pore Dilation Kinetics and Hydrophobic Gating of Magnesium Transport in the Cora System Biophysical Journal. 100: 91a. DOI: 10.1016/J.Bpj.2010.12.701  0.379
2011 Nikolic A, Pomès R. Molecular Simulation Study of Prion Peptide Self-Aggregation in the Presence of Lipid Membranes Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.3679  0.437
2011 Huynh L, Neale C, Pomès R, Allen C. Rational Design of Unimolecular Star Copolymer Micelles for Drug Delivery: Molecular Dynamics Study of Solvation, Aggregation, and Drug Binding Properties Biophysical Journal. 100: 310a. DOI: 10.1016/J.Bpj.2010.12.1895  0.364
2011 Li G, Pomès R. Molecular Mechanism of Aβ Amyloid Inhibition by Inositol Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.1369  0.321
2011 Kulleperuma K, Holyoake J, Pomès R. A general and Efficient All-Atom Simulation Method to Determine the Equilibrium Orientation of Transmembrane Proteins in Membranes Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.1323  0.353
2011 Neale C, Pomès R. Computer Simulation Studies of an Antimicrobial Peptide and a Microbial Virulence Factor: Statistical Convergence of Equilibrium Properties from Massive Sampling Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.1283  0.414
2011 Madill CA, Patel A, Saldaña M, Chow P, Pomès R. A Heterogeneous, Purpose Built Computer Architecture for Accelerating Biomolecular Simulation Biophysical Journal. 100: 1-9. DOI: 10.1016/J.Bpj.2010.12.1021  0.315
2010 Cuesta-Seijo JA, Neale C, Khan MA, Moktar J, Tran CD, Bishop RE, Pomès R, Privé GG. PagP crystallized from SDS/cosolvent reveals the route for phospholipid access to the hydrocarbon ruler. Structure (London, England : 1993). 18: 1210-9. PMID 20826347 DOI: 10.1016/J.Str.2010.06.014  0.317
2010 Nachman J, Gish G, Virag C, Pawson T, Pomès R, Pai E. Conformational determinants of phosphotyrosine peptides complexed with the Src SH2 domain. Plos One. 5: e11215. PMID 20574521 DOI: 10.1371/Journal.Pone.0011215  0.395
2010 Rauscher S, Pomès R. Molecular simulations of protein disorder. Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire. 88: 269-90. PMID 20453929 DOI: 10.1139/o09-169  0.672
2010 Chakrabarti N, Neale C, Payandeh J, Pai EF, Pomès R. An iris-like mechanism of pore dilation in the CorA magnesium transport system. Biophysical Journal. 98: 784-92. PMID 20197031 DOI: 10.1016/J.Bpj.2009.11.009  0.393
2010 Kurylowicz M, Yu CH, Pomès R. Systematic study of anharmonic features in a principal component analysis of gramicidin A. Biophysical Journal. 98: 386-95. PMID 20141751 DOI: 10.1016/J.Bpj.2009.10.034  0.327
2010 Huynh L, Neale C, Pomès R, Allen C. Systematic design of unimolecular star copolymer micelles using molecular dynamics simulations Soft Matter. 6: 5491. DOI: 10.1039/C001988G  0.37
2010 Holyoake J, Privé G, Pomès R. Molecular Basis for the Solvation and Reconstructive Denaturation of Proteins by Detergents Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.2360  0.415
2010 Li G, Pomès R. Molecular Mechanism of Inhibition of Amyloid Formation by Inositol Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.3556  0.331
2010 Neale C, Pomès R. Solvation and Binding of the Membrane Enzyme Pagp By Detergents and Lipids Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.297  0.389
2010 Nikolic A, Baud S, Rauscher S, Pomès R. Molecular Basis for the Catalysis of B-Sheet Formation by Water-Nonpolar Interfaces Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.1368  0.735
2009 Rauscher S, Neale C, Pomès R. Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling. Journal of Chemical Theory and Computation. 5: 2640-62. PMID 26631779 DOI: 10.1021/Ct900302N  0.692
2009 Henry RM, Yu CH, Rodinger T, Pomès R. Functional hydration and conformational gating of proton uptake in cytochrome c oxidase. Journal of Molecular Biology. 387: 1165-85. PMID 19248790 DOI: 10.1016/J.Jmb.2009.02.042  0.367
2008 Fadda E, Yu CH, Pomès R. Electrostatic control of proton pumping in cytochrome c oxidase. Biochimica Et Biophysica Acta. 1777: 277-84. PMID 18177731 DOI: 10.1016/J.Bbabio.2007.11.010  0.583
2007 Khan MA, Neale C, Michaux C, Pomès R, Privé GG, Woody RW, Bishop RE. Gauging a hydrocarbon ruler by an intrinsic exciton probe. Biochemistry. 46: 4565-79. PMID 17375935 DOI: 10.1021/Bi602526K  0.315
2006 Rauscher S, Baud S, Miao M, Keeley FW, Pomès R. Proline and glycine control protein self-organization into elastomeric or amyloid fibrils. Structure (London, England : 1993). 14: 1667-76. PMID 17098192 DOI: 10.1016/J.Str.2006.09.008  0.72
2006 Fadda E, Chakrabarti N, Pomès R. Reply to "Comment on acidity of a Cu-bound histidine in the binuclear center of cytochrome c oxidase", Journal of Physical Chemistry B. 110: 17288-17289. DOI: 10.1021/Jp0680286  0.52
2005 Fadda E, Chakrabarti N, Pomès R. Acidity of a Cu-bound histidine in the binuclear center of cytochrome C oxidase. The Journal of Physical Chemistry. B. 109: 22629-40. PMID 16853946 DOI: 10.1021/Jp052734+  0.584
2005 Rodinger T, Howell PL, Pomès R. Absolute free energy calculations by thermodynamic integration in four spatial dimensions. The Journal of Chemical Physics. 123: 34104. PMID 16080727 DOI: 10.1063/1.1946750  0.344
2005 Rodinger T, Pomès R. Enhancing the accuracy, the efficiency and the scope of free energy simulations. Current Opinion in Structural Biology. 15: 164-70. PMID 15837174 DOI: 10.1016/J.Sbi.2005.03.001  0.317
2004 Chakrabarti N, Roux B, Pomès R. Structural determinants of proton blockage in aquaporins. Journal of Molecular Biology. 343: 493-510. PMID 15451676 DOI: 10.1016/J.Jmb.2004.08.036  0.534
2004 Chakrabarti N, Tajkhorshid E, Roux B, Pomès R. Molecular basis of proton blockage in aquaporins. Structure (London, England : 1993). 12: 65-74. PMID 14725766 DOI: 10.1016/J.Str.2003.11.017  0.525
2003 Yu CH, Pomès R. Functional dynamics of ion channels: modulation of proton movement by conformational switches. Journal of the American Chemical Society. 125: 13890-4. PMID 14599229 DOI: 10.1021/Ja0353208  0.386
2003 Pomès R, Yu CH. Relay and blockage of protons in water chains. Frontiers in Bioscience : a Journal and Virtual Library. 8: d1288-97. PMID 12957853 DOI: 10.2741/1176  0.391
2003 Yu CH, Cukierman S, Pomès R. Theoretical study of the structure and dynamic fluctuations of dioxolane-linked gramicidin channels. Biophysical Journal. 84: 816-31. PMID 12547766 DOI: 10.1016/S0006-3495(03)74901-7  0.438
2002 Pomès R, Roux B. Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel. Biophysical Journal. 82: 2304-16. PMID 11964221 DOI: 10.1016/S0006-3495(02)75576-8  0.512
2001 Schumaker MF, Pomès R, Roux B. Framework model for single proton conduction through gramicidin. Biophysical Journal. 80: 12-30. PMID 11159380 DOI: 10.1016/S0006-3495(01)75992-9  0.479
2000 Schumaker MF, Pomès R, Roux B. A combined molecular dynamics and diffusion model of single proton conduction through gramicidin. Biophysical Journal. 79: 2840-57. PMID 11106593 DOI: 10.1016/S0006-3495(00)76522-2  0.516
1999 Pomès R, Eisenmesser E, Post CB, Roux B. Calculating excess chemical potentials using dynamic simulations in the fourth dimension The Journal of Chemical Physics. 111: 3387-3395. DOI: 10.1063/1.479622  0.49
1999 Pomès R. Theoretical Studies of the Grotthuss Mechanism in Biological Proton Wires Israel Journal of Chemistry. 39: 387-395. DOI: 10.1002/Ijch.199900044  0.399
1998 Pomès R, Roux B. Free energy profiles for H+ conduction along hydrogen-bonded chains of water molecules. Biophysical Journal. 75: 33-40. PMID 9649365 DOI: 10.1016/S0006-3495(98)77492-2  0.519
1998 Pomès R, Hummer G, Wikström M. Structure and dynamics of a proton shuttle in cytochrome c oxidase Biochimica Et Biophysica Acta. 1365: 255-260. DOI: 10.1016/S0005-2728(98)00077-2  0.429
1996 Roux B, Nina M, Pomès R, Smith JC. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophysical Journal. 71: 670-81. PMID 8842206 DOI: 10.1016/S0006-3495(96)79267-6  0.611
1996 Pomès R, Roux B. Structure and dynamics of a proton wire: a theoretical study of H+ translocation along the single-file water chain in the gramicidin A channel. Biophysical Journal. 71: 19-39. PMID 8804586 DOI: 10.1016/S0006-3495(96)79211-1  0.515
1995 Pomès R, Willson RC, McCammon JA. Free energy simulations of the HyHEL-10/HEL antibody-antigen complex. Protein Engineering. 8: 663-75. PMID 8577695 DOI: 10.1093/protein/8.7.663  0.392
1995 Pomès R, Roux B. Quantum effects on the structure and energy of a protonated linear chain of hydrogen-bonded water molecules Chemical Physics Letters. 234: 416-424. DOI: 10.1016/0009-2614(95)00071-B  0.489
1990 Pomès R, McCammon JA. Mass and step length optimization for the calculation of equilibrium properties by molecular dynamics simulation Chemical Physics Letters. 166: 425-428. DOI: 10.1016/0009-2614(90)85055-H  0.42
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