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List of works by Peter A. Kollman

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

article

A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP.

scientific article published on February 2002

A theoretical study of tautomerism in the gas phase and aqueous solution: a combined use of state-of-the-art ab initio quantum mechanics and free energy-perturbation methods

scholarly article by Piotr Cieplak et al published October 1987 in Journal of the American Chemical Society

AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

scientific article published in 1981

An all atom force field for simulations of proteins and nucleic acids

scientific article published in April 1986

Automatic parameterization of force field by systematic search and genetic algorithms

Chelate effect in cyclodextrin dimers: a computational (MD, MM/PBSA, and MM/GBSA) study

scientific article published in March 2006

Closing of the Nucleotide Pocket of Kinesin-Family Motors upon Binding to Microtubules ⬇️

scientific article published on May 2, 2003

Combinedab initioand Free Energy Calculations To Study Reactions in Enzymes and Solution: Amide Hydrolysis in Trypsin and Aqueous Solution

article

Computational Studies of Enzyme-Catalyzed Reactions:  Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis?

scientific article (publication date: February 2002)

Computational alanine scanning of the 1:1 human growth hormone-receptor complex

scientific article

Conformational preferences of substituted prolines in the collagen triple helix

scientific article published in July 2002

Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9.

scientific article published in September 2003

Elucidating the Origin of Conformational Energy Differences in Substituted 1,3-Dioxanes: A Combined Theoretical and Experimental Study

scientific article published in May 1996

Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces

scientific article published in May 2004

Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

scientific article

Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA.

scientific article

Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations

scientific article

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

article published in 2004

Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design

scientific article

Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement

scientific article

Multidimensional free-energy calculations using the weighted histogram analysis method

article by Shankar Kumar et al published November 1995 in Journal of Computational Chemistry

New-generation amber united-atom force field

scientific article published in July 2006

Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations

scientific article published in November 2004

QM−FE and Molecular Dynamics Calculations on CatecholO-Methyltransferase:  Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction

scientific article (publication date: March 2000)

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models

Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation

scientific article published in June 2002

Solvation Model Based on Weighted Solvent Accessible Surface Area

Symposium 1: Structure and engineering of proteins: New developments

scholarly article by Hartmut Michel et al published January 1990 in Analytical and Bioanalytical Chemistry

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

article

The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): a QM/FE approach

scientific article published in January 2003

pKa, MM, and QM studies of mechanisms of beta-lactamases and penicillin-binding proteins: acylation step

scientific article published in December 2002

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