Peter A. Kollman

Publication Activity (10 Years)

Years Active: 1987-2005
Publications (10 Years): 0

Publications

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. J. Comput. Chem. 26 (1) (2005)
Bernd Kuhn, Peter A. Kollman, Martin Stahl
Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations. J. Comput. Chem. 25 (15) (2004)
Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case
Development and testing of a general amber force field. J. Comput. Chem. 25 (9) (2004)
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. J. Comput. Chem. 24 (16) (2003)
Giuliano Alagona, Caterina Ghio, Peter A. Kollman
The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach. J. Comput. Chem. 24 (1) (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. J. Comput. Chem. 24 (12) (2003)
Shuanghong Huo, Irina Massova, Peter A. Kollman
Computational alanine scanning of the 1: 1 human growth hormone-receptor complex. J. Comput. Chem. 23 (1) (2002)
Irina Massova, Peter A. Kollman
pKa, MM, and QM studies of mechanisms of -lactamases and penicillin-binding proteins: Acylation step. J. Comput. Chem. 23 (16) (2002)
Junmei Wang, Peter A. Kollman
Automatic parameterization of force field by systematic search and genetic algorithms. J. Comput. Chem. 22 (12) (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. J. Comput. Aided Mol. Des. 15 (2) (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. J. Comput. Chem. 22 (10) (2001)
Yong Duan, Peter A. Kollman
Computational protein folding: From lattice to all-atom. IBM Syst. J. 40 (2) (2001)
Xavier Grabuleda, Carlos Jaime, Peter A. Kollman
Molecular dynamics simulation studies of liquid acetonitrile: New six-site model. J. Comput. Chem. 21 (10) (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? J. Comput. Chem. 21 (12) (2000)
Margaret A. McCarrick, Peter A. Kollman
Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations. J. Comput. Aided Mol. Des. 13 (2) (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. J. Comput. Aided Mol. Des. 12 (3) (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. J. Comput. Chem. 18 (7) (1997)
Richard W. Dixon, Peter A. Kollman
Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics. J. Comput. Chem. 18 (13) (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. J. Comput. Chem. 17 (9) (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. J. Comput. Chem. 17 (13) (1996)
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. J. Comput. Chem. 16 (11) (1995)
Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, Peter A. Kollman
Multidimensional Free-Energy Calculations Using the Weighted Histogram Analysis Method. J. Comput. Chem. 16 (11) (1995)
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. J. Comput. Chem. 16 (2) (1995)
Yaxiong Sun, Peter A. Kollman
Hydrophobic Solvation of Methane and Nonbond Parameters of the TIP3P Water Model. J. Comput. Chem. 16 (9) (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. J. Comput. Chem. 16 (12) (1995)
Peter D. J. Grootenhuis, Diana C. Roe, Peter A. Kollman, Irwin D. Kuntz
Finding potential DNA-binding compounds by using molecular shape. J. Comput. Aided Mol. Des. 8 (6) (1994)
Stephen E. DeBolt, David A. Pearlman, Peter A. Kollman
Free Energy Peturbation Calculations on Parallel Computers: Demonstrations of Scalable Linear Speedup. J. Comput. Chem. 15 (3) (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. J. Comput. Aided Mol. Des. 7 (3) (1993)
Jeanmarie Guenot, Peter A. Kollman
Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation. J. Comput. Chem. 14 (3) (1993)
Stephen E. DeBolt, Peter A. Kollman
AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed-memory hypercube computers. J. Comput. Chem. 14 (3) (1993)
Svein G. Dahl, Peter A. Kollman, Shashidhar N. Rao, U. Chandra Singh
Structural changes by sulfoxidation of phenothiazine drugs. J. Comput. Aided Mol. Des. 6 (3) (1992)
Peter A. Kollman
Grand challenges in computational science: Simulations on biological macromolecules. Future Gener. Comput. Syst. 5 (2-3) (1989)
Donald B. Boyd, Peter A. Kollman
Announcement. J. Comput. Aided Mol. Des. 1 (3) (1987)