Publications

Selected Publications

1. 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, and Liu AB.

J Chem Theory Comput. in press

2. 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]

3. 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]

4. 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]

5. 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]

6. 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]

7. 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]