Peter A. Kollman

33 papers Journal 33

Year	Rank	Type	Title / Venue / Authors
2005	J	`jnl`	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. Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case
2004	J	`jnl`	Development and testing of a general amber force field. J. Comput. Chem. Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case
2004	J	`jnl`	Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations. J. Comput. Chem. Bernd Kuhn, Peter A. Kollman, Martin Stahl
2003	J	`jnl`	A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Tai-Sung Lee, James W. Caldwell, Junmei Wang, Peter A. Kollman
2003	J	`jnl`	Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. J. Comput. Chem. Lillian T. Chong, Pradipta Bandyopadhyay, Thomas S. Scanlan, Irwin D. Kuntz, Peter A. Kollman
2003	J	`jnl`	The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach. J. Comput. Chem. Giuliano Alagona, Caterina Ghio, Peter A. Kollman
2002	J	`jnl`	Computational alanine scanning of the 1: 1 human growth hormone-receptor complex. J. Comput. Chem. Shuanghong Huo, Irina Massova, Peter A. Kollman
2002	J	`jnl`	pKa, MM, and QM studies of mechanisms of -lactamases and penicillin-binding proteins: Acylation step. J. Comput. Chem. Irina Massova, Peter A. Kollman
2001	J	`jnl`	Automatic parameterization of force field by systematic search and genetic algorithms. J. Comput. Chem. Junmei Wang, Peter A. Kollman
2001	J	`jnl`	Computational protein folding: From lattice to all-atom. IBM Syst. J. Yong Duan, Peter A. Kollman
2001	J	`jnl`	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. Lu Wang, Yong Duan, Pieter F. W. Stouten, George V. De Lucca, Ronald M. Klabe, Peter A. Kollman
2001	J	`jnl`	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. Piotr Cieplak, James W. Caldwell, Peter A. Kollman
2000	J	`jnl`	How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. Junmei Wang, Piotr Cieplak, Peter A. Kollman
2000	J	`jnl`	Molecular dynamics simulation studies of liquid acetonitrile: New six-site model. J. Comput. Chem. Xavier Grabuleda, Carlos Jaime, Peter A. Kollman
1999	J	`jnl`	Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations. J. Comput. Aided Mol. Des. Margaret A. McCarrick, Peter A. Kollman
1998	J	`jnl`	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. Randall J. Radmer, Peter A. Kollman
1997	J	`jnl`	Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics. J. Comput. Chem. Richard W. Dixon, Peter A. Kollman
1997	J	`jnl`	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. Randall J. Radmer, Peter A. Kollman
1996	J	`jnl`	Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions. J. Comput. Chem. Christophe Chipot, Peter A. Kollman, David A. Pearlman
1996	J	`jnl`	Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics. J. Comput. Chem. Wendy D. Cornell, Maria P. Ha, Yax Sun, Peter A. Kollman
1995	J	`jnl`	A Molecular Mechanical Model That Reproduces the Relative Energies for Chair and Twist-Boat Conformations of 1, 3-Dioxanes. J. Comput. Chem. Allison E. Howard, Piotr Cieplak, Peter A. Kollman
1995	J	`jnl`	Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and Proteins. J. Comput. Chem. Piotr Cieplak, Wendy D. Cornell, Christopher I. Bayly, Peter A. Kollman
1995	J	`jnl`	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. Alain St.-Amant, Wendy D. Cornell, Peter A. Kollman, Thomas A. Halgren
1995	J	`jnl`	Hydrophobic Solvation of Methane and Nonbond Parameters of the TIP3P Water Model. J. Comput. Chem. Yaxiong Sun, Peter A. Kollman
1995	J	`jnl`	Multidimensional Free-Energy Calculations Using the Weighted Histogram Analysis Method. J. Comput. Chem. Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, Peter A. Kollman
1994	J	`jnl`	Finding potential DNA-binding compounds by using molecular shape. J. Comput. Aided Mol. Des. Peter D. J. Grootenhuis, Diana C. Roe, Peter A. Kollman, Irwin D. Kuntz
1994	J	`jnl`	Free Energy Peturbation Calculations on Parallel Computers: Demonstrations of Scalable Linear Speedup. J. Comput. Chem. Stephen E. DeBolt, David A. Pearlman, Peter A. Kollman
1993	J	`jnl`	AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed-memory hypercube computers. J. Comput. Chem. Stephen E. DeBolt, Peter A. Kollman
1993	J	`jnl`	Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation. J. Comput. Chem. Jeanmarie Guenot, Peter A. Kollman
1993	J	`jnl`	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. Piotr Cieplak, Peter A. Kollman
1992	J	`jnl`	Structural changes by sulfoxidation of phenothiazine drugs. J. Comput. Aided Mol. Des. Svein G. Dahl, Peter A. Kollman, Shashidhar N. Rao, U. Chandra Singh
1989	J	`jnl`	Grand challenges in computational science: Simulations on biological macromolecules. Future Gener. Comput. Syst. Peter A. Kollman
1987	J	`jnl`	Announcement. J. Comput. Aided Mol. Des. Donald B. Boyd, Peter A. Kollman