Announcement. - Donald B. Boyd; Peter A. Kollman (J. Comput. Aided Mol. Des., 1987)

Grand challenges in computational science: Simulations on biological macromolecules. - Peter A. Kollman (Future Gener. Comput. Syst., 1989)

Structural changes by sulfoxidation of phenothiazine drugs. - Svein G. Dahl; Peter A. Kollman; Shashidhar N. Rao; U. Chandra Singh (J. Comput. Aided Mol. Des., 1992)

Peptide mimetics as enzyme inhibitors: Use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor. - Piotr Cieplak; Peter A. Kollman (J. Comput. Aided Mol. Des., 1993)

AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed-memory hypercube computers. - Stephen E. DeBolt; Peter A. Kollman (J. Comput. Chem., 1993)

Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation. - Jeanmarie Guenot; Peter A. Kollman (J. Comput. Chem., 1993)

Finding potential DNA-binding compounds by using molecular shape. - Peter D. J. Grootenhuis; Diana C. Roe; Peter A. Kollman; Irwin D. Kuntz (J. Comput. Aided Mol. Des., 1994)

Free Energy Peturbation Calculations on Parallel Computers: Demonstrations of Scalable Linear Speedup. - Stephen E. DeBolt; David A. Pearlman; Peter A. Kollman (J. Comput. Chem., 1994)

Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and Proteins. - Piotr Cieplak; Wendy D. Cornell; Christopher I. Bayly; Peter A. Kollman (J. Comput. Chem., 1995)

A Molecular Mechanical Model That Reproduces the Relative Energies for Chair and Twist-Boat Conformations of 1, 3-Dioxanes. - Allison E. Howard; Piotr Cieplak; Peter A. Kollman (J. Comput. Chem., 1995)

Multidimensional Free-Energy Calculations Using the Weighted Histogram Analysis Method. - Shankar Kumar; John M. Rosenberg; Djamal Bouzida; Robert H. Swendsen; Peter A. Kollman (J. Comput. Chem., 1995)

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. - Alain St.-Amant; Wendy D. Cornell; Peter A. Kollman; Thomas A. Halgren (J. Comput. Chem., 1995)

Hydrophobic Solvation of Methane and Nonbond Parameters of the TIP3P Water Model. - Yaxiong Sun; Peter A. Kollman (J. Comput. Chem., 1995)

Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions. - Christophe Chipot; Peter A. Kollman; David A. Pearlman (J. Comput. Chem., 1996)

Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics. - Wendy D. Cornell; Maria P. Ha; Yax Sun; Peter A. Kollman (J. Comput. Chem., 1996)

Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics. - Richard W. Dixon; Peter A. Kollman (J. Comput. Chem., 1997)

Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes. - Randall J. Radmer; Peter A. Kollman (J. Comput. Chem., 1997)

The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors. - Randall J. Radmer; Peter A. Kollman (J. Comput. Aided Mol. Des., 1998)

Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations. - Margaret A. McCarrick; Peter A. Kollman (J. Comput. Aided Mol. Des., 1999)

Molecular dynamics simulation studies of liquid acetonitrile: New six-site model. - Xavier Grabuleda; Carlos Jaime; Peter A. Kollman (J. Comput. Chem., 2000)

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? - Junmei Wang; Piotr Cieplak; Peter A. Kollman (J. Comput. Chem., 2000)

Computational protein folding: From lattice to all-atom. - Yong Duan; Peter A. Kollman (IBM Syst. J., 2001)

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. - Lu Wang; Yong Duan; Pieter F. W. Stouten; George V. De Lucca; Ronald M. Klabe; Peter A. Kollman (J. Comput. Aided Mol. Des., 2001)

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. - Piotr Cieplak; James W. Caldwell; Peter A. Kollman (J. Comput. Chem., 2001)

Automatic parameterization of force field by systematic search and genetic algorithms. - Junmei Wang; Peter A. Kollman (J. Comput. Chem., 2001)

Computational alanine scanning of the 1: 1 human growth hormone-receptor complex. - Shuanghong Huo; Irina Massova; Peter A. Kollman (J. Comput. Chem., 2002)

pKa, MM, and QM studies of mechanisms of -lactamases and penicillin-binding proteins: Acylation step. - Irina Massova; Peter A. Kollman (J. Comput. Chem., 2002)

The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach. - Giuliano Alagona; Caterina Ghio; Peter A. Kollman (J. Comput. Chem., 2003)

Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. - Lillian T. Chong; Pradipta Bandyopadhyay; Thomas S. Scanlan; Irwin D. Kuntz; Peter A. Kollman (J. Comput. Chem., 2003)

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. - Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C. Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo 001; Tai-Sung Lee; James W. Caldwell; Junmei Wang; et al. (J. Comput. Chem., 2003)

Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations. - Bernd Kuhn; Peter A. Kollman; Martin Stahl (J. Comput. Chem., 2004)

Development and testing of a general amber force field. - Junmei Wang; Romain M. Wolf; James W. Caldwell; Peter A. Kollman; David A. Case (J. Comput. Chem., 2004)

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. - Junmei Wang; Romain M. Wolf; James W. Caldwell; Peter A. Kollman; David A. Case (J. Comput. Chem., 2005)