Sergei Y. Ponomarev - Publications

2007 Wesleyan University, Middletown, CT, United States 

13 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2014 Li X, Ponomarev SY, Sigalovsky DL, Cvitkovic JP, Kaminski GA. POSSIM: Parameterizing Complete Second-Order Polarizable Force Field for Proteins. Journal of Chemical Theory and Computation. 10: 4896-4910. PMID 25400518 DOI: 10.1021/ct500243k  0.84
2013 Li X, Ponomarev SY, Sa Q, Sigalovsky DL, Kaminski GA. Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues. Journal of Computational Chemistry. 34: 1241-50. PMID 23420678 DOI: 10.1002/jcc.23248  0.84
2012 Ponomarev SY, Sa Q, Kaminski GA. Effects of lysine substitution on stability of polyalanine alpha-helix. Journal of Chemical Theory and Computation. 8: 4691-4706. PMID 23483820 DOI: 10.1021/ct300492n  0.84
2012 Click TH, Ponomarev SY, Kaminski GA. Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ. Journal of Computational Chemistry. 33: 1142-51. PMID 22370900 DOI: 10.1002/jcc.22944  0.84
2011 Ponomarev SY, Click TH, Kaminski GA. Electrostatic polarization is crucial in reproducing Cu(I) interaction energies and hydration. The Journal of Physical Chemistry. B. 115: 10079-85. PMID 21761909 DOI: 10.1021/jp2051933  0.84
2011 Ponomarev SY, Kaminski GA. Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone. Journal of Chemical Theory and Computation. 7: 1415-1427. PMID 21743799 DOI: 10.1021/ct1007197  0.84
2011 Ponomarev SY, Audie J. Computational prediction and analysis of the DR6-NAPP interaction. Proteins. 79: 1376-95. PMID 21337622 DOI: 10.1002/prot.22962  0.84
2009 Kaminski GA, Ponomarev SY, Liu AB. Polarizable Simulations with Second order Interaction Model - force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations. Journal of Chemical Theory and Computation. 5: 2935-2943. PMID 20209038 DOI: 10.1021/ct900409p  0.84
2009 Ponomarev SY, Putkaradze V, Bishop TC. Relaxation dynamics of nucleosomal DNA. Physical Chemistry Chemical Physics : Pccp. 11: 10633-43. PMID 20145808 DOI: 10.1039/b910937b  0.84
2009 Sen S, Andreatta D, Ponomarev SY, Beveridge DL, Berg MA. Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments. Journal of the American Chemical Society. 131: 1724-35. PMID 19191698 DOI: 10.1021/ja805405a  0.84
2008 Knee KM, Dixit SB, Aitken CE, Ponomarev S, Beveridge DL, Mukerji I. Spectroscopic and molecular dynamics evidence for a sequential mechanism for the A-to-B transition in DNA. Biophysical Journal. 95: 257-72. PMID 18326653 DOI: 10.1529/biophysj.107.117606  0.84
2006 Dixit SB, Ponomarev SY, Beveridge DL. Root mean square deviation probability analysis of molecular dynamics trajectories on DNA. Journal of Chemical Information and Modeling. 46: 1084-93. PMID 16711728 DOI: 10.1021/ci0504925  0.84
2004 Ponomarev SY, Thayer KM, Beveridge DL. Ion motions in molecular dynamics simulations on DNA. Proceedings of the National Academy of Sciences of the United States of America. 101: 14771-5. PMID 15465909 DOI: 10.1073/pnas.0406435101  0.84
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