Publications

Designed by Sergei Y. Ponomarev sponomarev@wpi.edu and George A. Kaminski gkaminski@wpi.edu

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	Selected Publications Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for side-chain analogues Li X, Ponomarev SY, Sa Q, Sigalovsky DL, Kaminski GA. J Comput Chem, accepted for publication [PubMed ID NIHMS444236]. Effects of Lysine Substitution on Stability of Polyalanine alpha-Helix Ponomarev SY, Sa Q, Kaminski GA. J Chem Theory Comput. 2012; 8(11): 4691-4706. [PubMed - pending] Calculating pK(a) values for substituted phenols and hydration energies for other compounds with the first-order fuzzy-border continuum solvation model. Sharma I, Kaminski GA. J Comput Chem. 2012 Nov 15;33(30):2388-99. doi: 10.1002/jcc.23074. Epub 2012 Jul 19.PMID: 22815192 [PubMed - in process] Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ. Click TH, Ponomarev SY, Kaminski GA. J Comput Chem. 2012 Apr 30;33(11):1142-51. doi: 10.1002/jcc.22944. Epub 2012 Feb 27.PMID: 22370900 [PubMed - indexed for MEDLINE] Electrostatic polarization is crucial in reproducing Cu(I) interaction energies and hydration. Ponomarev SY, Click TH, Kaminski GA. J Phys Chem B. 2011 Aug 25;115(33):10079-85. Epub 2011 Jul 28.PMID: 21761909 [PubMed - indexed for MEDLINE] Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone. Ponomarev SY, Kaminski GA. J Chem Theory Comput. 2011 May 10;7(5):1415-1427.PMID: 21743799 [PubMed] Quality of random number generators significantly affects results of Monte Carlo simulations for organic and biological systems. Click TH, Liu A, Kaminski GA. J Comput Chem. 2011 Feb;32(3):513-24. doi: 10.1002/jcc.21638. Epub 2010 Aug 23.PMID: 20734313 [PubMed - indexed for MEDLINE] Polarizable Simulations with Second order Interaction Model - force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations. Kaminski GA, Ponomarev SY, Liu AB. J Chem Theory Comput. 2009 Oct 5;5(11):2935-2943.PMID: 20209038 [PubMed] Reproducing basic pKa values for turkey ovomucoid third domain using a polarizable force field. Click TH, Kaminski GA. J Phys Chem B. 2009 Jun 4;113(22):7844-50.PMID: 19432439 [PubMed - indexed for MEDLINE] Computational Studies of the X-Link Inhibitor of Apoptosis Complex Formation with Caspase-9 and a Small Antagonist Kaminski GA. J Chem Theory Comput. 2008; 4(5): 847-854. Electrostatic polarization is crucial for reproducing pKa shifts of carboxylic residues in Turkey ovomucoid third domain. Macdermaid CM, Kaminski GA. J Phys Chem B. 2007 Aug 2;111(30):9036-44. Epub 2007 Jun 28.PMID: 17602581 [PubMed - indexed for MEDLINE] Accurate determination of pyridine-poly(amidoamine) dendrimer absolute binding constants with the OPLS-AA force field and direct integration of radial distribution functions. Peng Y, Kaminski GA. J Phys Chem B. 2005 Aug 11;109(31):15145-9.PMID: 16852916 [PubMed] Accurate prediction of absolute acidity constants in water with a polarizable force field: substituted phenols, methanol, and imidazole. Kaminski GA. J Phys Chem B. 2005 Mar 31;109(12):5884-90.PMID: 16851640 [PubMed - indexed for MEDLINE] A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations. Kaminski GA, Friesner RA, Zhou R. J Comput Chem. 2003 Feb;24(3):267-76.PMID: 12548718 [PubMed - indexed for MEDLINE] Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YX, Murphy RB, Zhou R, Halgren TA. J Comput Chem. 2002 Dec;23(16):1515-31.PMID: 12395421 [PubMed - indexed for MEDLINE]