Peter A. Kollman

Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case: Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, "Development and testing of a general amber force field" Journal of Computational Chemistry(2004) 25(9) 1157-1174. Journal of Computational Chemistry 26(1): 114- (2005)

Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case: Development and testing of a general amber force field. Journal of Computational Chemistry 25(9): 1157-1174 (2004)

Giuliano Alagona, Caterina Ghio, Peter A. Kollman: The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach. Journal of Computational Chemistry 24(1): 46-56 (2003)

Lillian T. Chong, Pradipta Bandyopadhyay, Thomas S. Scanlan, Irwin D. Kuntz, Peter A. Kollman: Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. Journal of Computational Chemistry 24(12): 1371-1377 (2003)

Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, James W. Caldwell, Junmei Wang, Peter A. Kollman: A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry 24(16): 1999-2012 (2003)

Shuanghong Huo, Irina Massova, Peter A. Kollman: Computational alanine scanning of the 1: 1 human growth hormone-receptor complex. Journal of Computational Chemistry 23(1): 15-27 (2002)

Irina Massova, Peter A. Kollman: pKa, MM, and QM studies of mechanisms of -lactamases and penicillin-binding proteins: Acylation step. Journal of Computational Chemistry 23(16): 1559-1576 (2002)

Yong Duan, Peter A. Kollman: Computational protein folding: From lattice to all-atom. IBM Systems Journal 40(2): 297-309 (2001)

Lu Wang, Yong Duan, Pieter F. W. Stouten, George V. De Lucca, Ronald M. Klabe, Peter A. Kollman: Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations. Journal of Computer-Aided Molecular Design 15(2): 145-156 (2001)

Piotr Cieplak, James W. Caldwell, Peter A. Kollman: Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases. Journal of Computational Chemistry 22(10): 1048-1057 (2001)

Junmei Wang, Peter A. Kollman: Automatic parameterization of force field by systematic search and genetic algorithms. Journal of Computational Chemistry 22(12): 1219-1228 (2001)

Xavier Grabuleda, Carlos Jaime, Peter A. Kollman: Molecular dynamics simulation studies of liquid acetonitrile: New six-site model. Journal of Computational Chemistry 21(10): 901-908 (2000)

Junmei Wang, Piotr Cieplak, Peter A. Kollman: How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? Journal of Computational Chemistry 21(12): 1049-1074 (2000)

Margaret A. McCarrick, Peter A. Kollman: Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations. Journal of Computer-Aided Molecular Design 13(2): 109-121 (1999)

Randall J. Radmer, Peter A. Kollman: The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors. Journal of Computer-Aided Molecular Design 12(3): 215-227 (1998)

Randall J. Radmer, Peter A. Kollman: Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes. Journal of Computational Chemistry 18(7): 902-919 (1997)

Richard W. Dixon, Peter A. Kollman: Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics. Journal of Computational Chemistry 18(13): 1632-1646 (1997)

Christophe Chipot, Peter A. Kollman, David A. Pearlman: Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions. Journal of Computational Chemistry 17(9): 1112-1131 (1996)

Wendy D. Cornell, Maria P. Ha, Yax Sun, Peter A. Kollman: Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics. Journal of Computational Chemistry 17(13): 1541-1548 (1996)

Allison E. Howard, Piotr Cieplak, Peter A. Kollman: A Molecular Mechanical Model That Reproduces the Relative Energies for Chair and Twist-Boat Conformations of 1, 3-Dioxanes. Journal of Computational Chemistry 16(2): 243-262 (1995)

Yaxiong Sun, Peter A. Kollman: Hydrophobic Solvation of Methane and Nonbond Parameters of the TIP3P Water Model. Journal of Computational Chemistry 16(9): 1164-1169 (1995)

Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, Peter A. Kollman: Multidimensional Free-Energy Calculations Using the Weighted Histogram Analysis Method. Journal of Computational Chemistry 16(11): 1339-1350 (1995)

Piotr Cieplak, Wendy D. Cornell, Christopher I. Bayly, Peter A. Kollman: Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and Proteins. Journal of Computational Chemistry 16(11): 1357-1376 (1995)

Alain St.-Amant, Wendy D. Cornell, Peter A. Kollman, Thomas A. Halgren: Calculation of Molecular Geometries, Relative Conformational Energies, Dipole Moments, and Molecular Electrostatic Potential Fitted Charges of Small Organic Molecules of Biochemical Interest by Density Function Theory. Journal of Computational Chemistry 16(12): 1483-1506 (1995)

Peter D. J. Grootenhuis, Diana C. Roe, Peter A. Kollman, Irwin D. Kuntz: Finding potential DNA-binding compounds by using molecular shape. Journal of Computer-Aided Molecular Design 8(6): 731-750 (1994)

Stephen E. DeBolt, David A. Pearlman, Peter A. Kollman: Free Energy Peturbation Calculations on Parallel Computers: Demonstrations of Scalable Linear Speedup. Journal of Computational Chemistry 15(3): 351-374 (1994)

Piotr Cieplak, Peter A. Kollman: Peptide mimetics as enzyme inhibitors: Use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor. Journal of Computer-Aided Molecular Design 7(3): 291-304 (1993)

Svein G. Dahl, Peter A. Kollman, Shashidhar N. Rao, U. Chandra Singh: Structural changes by sulfoxidation of phenothiazine drugs. Journal of Computer-Aided Molecular Design 6(3): 207-222 (1992)