Sergei Y. Ponomarev
Affiliations: | 2007 | Wesleyan University, Middletown, CT, United States |
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Sign in to add mentor| David L. Beveridge | grad student | 2007 | Wesleyan | |
| (Molecular dynamics simulation of DNA oligonucleotides.) | ||||
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Publications
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| Li X, Ponomarev SY, Sigalovsky DL, et al. (2014) POSSIM: Parameterizing Complete Second-Order Polarizable Force Field for Proteins. Journal of Chemical Theory and Computation. 10: 4896-4910 |
| Li X, Ponomarev SY, Sa Q, et al. (2013) Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues. Journal of Computational Chemistry. 34: 1241-50 |
| Ponomarev SY, Sa Q, Kaminski GA. (2012) Effects of lysine substitution on stability of polyalanine alpha-helix. Journal of Chemical Theory and Computation. 8: 4691-4706 |
| Click TH, Ponomarev SY, Kaminski GA. (2012) 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 |
| Ponomarev SY, Click TH, Kaminski GA. (2011) Electrostatic polarization is crucial in reproducing Cu(I) interaction energies and hydration. The Journal of Physical Chemistry. B. 115: 10079-85 |
| Ponomarev SY, Kaminski GA. (2011) 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 |
| Kaminski GA, Ponomarev SY, Liu AB. (2009) 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 |
| Ponomarev SY, Putkaradze V, Bishop TC. (2009) Relaxation dynamics of nucleosomal DNA. Physical Chemistry Chemical Physics : Pccp. 11: 10633-43 |
| Sen S, Andreatta D, Ponomarev SY, et al. (2009) 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 |
| Ponomarev SY, Bishop TC, Putkaradze V. (2009) DNA Relaxation Dynamics in 1ID3 Yeast Nucleosome MD Simulation Biophysical Journal. 96: 577a-578a |