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P. Kollman · SciRah

Researcher profile · Semantic Scholar

P. Kollman

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P. Kollman — researcher profile on SciRah

h-index: 92
Works: 423
Citations: 92K

Most-cited papers

Development and testing of a general amber force field
Jun-Mei Wang, R. Wolf, J. Caldwell, P. Kollman +1 more
2004Journal of Computational Chemistry18K citations Open access
Semantic Scholar
Automatic atom type and bond type perception in molecular mechanical calculations.
Jun-Mei Wang, Wei Wang, P. Kollman, D. Case
2006Journal of Molecular Graphics and Modelling5,175 citations
Semantic Scholar
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
P. Kollman, I. Massova, Carolina M. Reyes, B. Kuhn +11 more
2000Accounts of Chemical Research4,626 citations
Semantic Scholar
A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations
Y. Duan, Chun Wu, S. Chowdhury, Mathew C. Lee +9 more
2003Journal of Computational Chemistry4,244 citations
Semantic Scholar
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
Jun-Mei Wang, P. Cieplak, P. Kollman
2000Journal of Computational Chemistry3,472 citations
Semantic Scholar
Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
I. Massova, P. Kollman
2000899 citations
Semantic Scholar
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.
T. Cheatham, P. Cieplak, P. Kollman
1999Journal of Biomolecular Structure and Dynamics823 citations
Semantic Scholar
Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies
I. Massova, P. Kollman
1999749 citations
Semantic Scholar
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.
Jun-Mei Wang, P. Morin, Wei Wang, P. Kollman
2001Journal of the American Chemical Society687 citations
Semantic Scholar
Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions.
Wei Wang, O. Donini, Carolina M. Reyes, P. Kollman
2001Annual Review of Biophysics and Biomolecular Structure526 citations
Semantic Scholar
Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models.
B. Kuhn, P. Kollman
2000Journal of Medicinal Chemistry471 citations
Semantic Scholar
Molecular dynamics simulation of nucleic acids.
T. Cheatham, P. Kollman
2000Annual review of physical chemistry (Print)301 citations
Semantic Scholar
Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model.
Wei Wang, P. Kollman
2000Journal of Molecular Biology298 citations
Semantic Scholar
Computational alanine scanning of the 1:1 human growth hormone–receptor complex
Shuang-Hong Huo, I. Massova, P. Kollman
2002Journal of Computational Chemistry292 citations
Semantic Scholar
Lactonization is the critical first step in the disposition of the 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor atorvastatin.
W. Jacobsen, B. Kuhn, A. Soldner, G. Kirchner +4 more
2000Drug Metabolism And Disposition244 citations
Semantic Scholar
Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance
Wei Wang, P. Kollman
2001Proceedings of the National Academy of Sciences of the United States of America240 citations Open access
Semantic Scholar
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7.
L. Chong, Y. Duan, Lu Wang, I. Massova +1 more
1999Proceedings of the National Academy of Sciences of the United States of America234 citations Open access
Semantic Scholar
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
Jun-Mei Wang, R. Wolf, J. Caldwell, P. Kollman +1 more
2005Journal of Computational Chemistry226 citations
Semantic Scholar
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods.
H. Gouda, I. Kuntz, D. Case, P. Kollman
2003Biopolymers212 citations
Semantic Scholar
New-generation amber united-atom force field.
Li-Jiang Yang, Chunhu Tan, Meng-Juei Hsieh, Jun-Mei Wang +5 more
2006Journal of Physical Chemistry B183 citations
Semantic Scholar
Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design.
Shuang-Hong Huo, Jun-Mei Wang, P. Cieplak, P. Kollman +1 more
2002Journal of Medicinal Chemistry165 citations Open access
Semantic Scholar
Molecular dynamics in the endgame of protein structure prediction.
Matthew R. Lee, Jerry Tsai, David Baker, P. Kollman
2001Journal of Molecular Biology138 citations
Semantic Scholar
What determines the van der Waals coefficient β in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?
Wen Wang, Jian Wang, P. Kollman
1999Proteins: Structure, Function, and Bioinformatics130 citations Open access
Semantic Scholar
An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis.
W. Wang, W. Lim, A. Jakalian, J. Wang +3 more
2001Journal of the American Chemical Society125 citations
Semantic Scholar
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
P. Kollman
2001121 citations
Semantic Scholar
Automatic parameterization of force field by systematic search and genetic algorithms
Jun-Mei Wang, P. Kollman
2001Journal of Computational Chemistry119 citations
Semantic Scholar
Solvation Model Based on Weighted Solvent Accessible Surface Area
Jun-Mei Wang, Wei Wang, Shuang-Hong Huo, Matthew R. Lee +1 more
2001108 citations
Semantic Scholar
A Ligand That Is Predicted to Bind Better to Avidin than Biotin: Insights from Computational Fluorine Scanning
Bernd Kuhn, P. Kollman
2000108 citations
Semantic Scholar
Noncovalent interactions
P. Kollman
200895 citations
Semantic Scholar
Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations.
K. Masukawa, P. Kollman, I. Kuntz
2003Journal of Medicinal Chemistry95 citations
Semantic Scholar
Calculation and prediction of binding free energies for the matrix metalloproteinases.
O. Donini, P. Kollman
2000Journal of Medicinal Chemistry90 citations
Semantic Scholar
Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution.
P. Kollman, Bernd Kuhn, Oreola Donini, M. Peräkylä +2 more
2001Accounts of Chemical Research78 citations
Semantic Scholar
QM−FE and Molecular Dynamics Calculations on Catechol O-Methyltransferase: Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction
Bernd Kuhn, P. Kollman
200071 citations
Semantic Scholar
Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA.
Jun-Mei Wang, Xinshan Kang, I. Kuntz, P. Kollman
2005Journal of Medicinal Chemistry64 citations
Semantic Scholar
2.1 and 1.8 Å Average Cα RMSD Structure Predictions on Two Small Proteins, HP-36 and S15
Matthew R. Lee, D. Baker, P. Kollman
200162 citations
Semantic Scholar
Closing of the Nucleotide Pocket of Kinesin-Family Motors upon Binding to Microtubules
N. Naber, T. J. Minehardt, S. Rice, Xiao-Ru Chen +8 more
2003Science57 citations
Semantic Scholar
Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations
B. Kuhn, P. Kollman, M. Stahl
2004Journal of Computational Chemistry56 citations
Semantic Scholar
Computational protein folding: From lattice to all-atom
Y. Duan, P. Kollman
2001IBM Systems Journal53 citations
Semantic Scholar
Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces.
Edward Z Wen, Meng-Juei Hsieh, P. Kollman, Ray Luo
2004Journal of Molecular Graphics and Modelling43 citations
Semantic Scholar
Amber 2015, University of California, San Francisco
D. Case, J. Berryman, Robin M. Betz, D. Cerutti +36 more
201538 citations
Semantic Scholar
Conformational preferences of substituted prolines in the collagen triple helix.
S. Mooney, P. Kollman, Teri E. Klein
2002Biopolymers37 citations
Semantic Scholar
Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1
C. Simmerling, Matthew R. Lee, A. Ortiz, A. Kolinski +2 more
200037 citations
Semantic Scholar
Computed free energy differences between point mutations in a collagen-like peptide.
S. Mooney, Conrad C. Huang, P. Kollman, Teri E. Klein
2001Biopolymers36 citations
Semantic Scholar
CALCULATING THE ABSOLUTE FREE ENERGY OF ASSOCIATION OF NETROPSIN AND DNA
Suresh B. Singh, P. Kollman
199936 citations
Semantic Scholar
Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis?
P. Kollman, Bernd Kuhn, M. Peräkylä
200235 citations Open access
Semantic Scholar
A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP.
T. J. Minehardt, N. Marzari, R. Cooke, E. Pate +2 more
2002Biophysical Journal35 citations Open access
Semantic Scholar
Why Does Trypsin Cleave BPTI so Slowly
M. Peräkylä, P. Kollman
200035 citations
Semantic Scholar
Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction.
Matthew R. Lee, P. Kollman
2001Structure30 citations Open access
Semantic Scholar
Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method
David E. Konerding, Thomas E. Iii Cheatham, P. Kollman, T. L. James
1999Journal of Biomolecular NMR30 citations
Semantic Scholar
Theoretical and experimental studies of biotin analogues that bind almost as tightly to streptavidin as biotin.
Richard W. Dixon, Randall J. Radmer, B. Kuhn, P. Kollman +8 more
2002Journal of Organic Chemistry25 citations
Semantic Scholar

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