Peter A Kollman

Peter A Kollman

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Peter A Kollman

Peter A Kollman

Publications by authors named "Peter A Kollman"

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22Publications

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Automatic atom type and bond type perception in molecular mechanical calculations.

J Mol Graph Model 2006 Oct 3;25(2):247-60. Epub 2006 Feb 3.

College of Chemistry, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1016/j.jmgm.2005.12.005DOI Listing
October 2006

New-generation amber united-atom force field.

J Phys Chem B 2006 Jul;110(26):13166-76

Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA.

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http://dx.doi.org/10.1021/jp060163vDOI Listing
July 2006

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

J Org Chem 2006 Mar;71(5):2056-63

Departament de Química, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1021/jo052469oDOI Listing
March 2006

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

J Med Chem 2005 Apr;48(7):2432-44

Encysive Pharmaceuticals Inc., 7000 Fannin, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1021/jm049606eDOI Listing
April 2005

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

J Comput Chem 2004 Nov;25(15):1865-72

Molecular Design, Pharmaceutical Division, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland.

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http://doi.wiley.com/10.1002/jcc.20111
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http://dx.doi.org/10.1002/jcc.20111DOI Listing
November 2004

Development and testing of a general amber force field.

J Comput Chem 2004 Jul;25(9):1157-74

Encysive Pharmaceuticals Inc., 7000 Fannin, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1002/jcc.20035DOI Listing
July 2004

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

J Mol Graph Model 2004 May;22(5):415-24

Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA.

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http://dx.doi.org/10.1016/j.jmgm.2003.12.008DOI Listing
May 2004

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

J Med Chem 2003 Dec;46(26):5628-37

Department of Pharmaceutical Chemistry, Chemistry and Chemical Biology Program, University of California-San Francisco, 600 16th Street, Box 2240, San Francisco, CA 94143-2240, USA.

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http://dx.doi.org/10.1021/jm030060qDOI Listing
December 2003

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

J Comput Chem 2003 Sep;24(12):1371-7

Graduate Group in Biophysics and Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94143-2240, USA.

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http://dx.doi.org/10.1002/jcc.10293DOI Listing
September 2003

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

J Comput Chem 2003 Jan;24(1):46-56

CNR-IPCF, Istituto per i Processi Chimico-Fisici, Molecular Modeling Lab, Via Moruzzi 1, I-56124 Pisa, Italy.

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http://dx.doi.org/10.1002/jcc.10153DOI Listing
January 2003

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

Biopolymers 2003 Jan;68(1):16-34

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.

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http://doi.wiley.com/10.1002/bip.10270
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http://dx.doi.org/10.1002/bip.10270DOI Listing
January 2003

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

J Comput Chem 2002 Dec;23(16):1559-76

Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143-0446, USA.

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http://dx.doi.org/10.1002/jcc.10129DOI Listing
December 2002

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

J Am Chem Soc 2002 Oct;124(42):12535-42

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-0446, USA.

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October 2002

Conformational preferences of substituted prolines in the collagen triple helix.

Biopolymers 2002 Jul;64(2):63-71

Stanford Medical Informatics, 251 Campus Drive, MSOB X-215, Stanford University, Stanford, CA 94305-5479, USA.

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http://dx.doi.org/10.1002/bip.10123DOI Listing
July 2002

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

Proteins 2002 Jun;47(4):469-80

Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, Zürich, Switzerland.

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http://dx.doi.org/10.1002/prot.10046DOI Listing
June 2002

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

J Med Chem 2002 Mar;45(7):1412-9

Department of Pharmaceutical Chemistry, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143-0446, USA.

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March 2002

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

J Comput Chem 2002 Jan;23(1):15-27

Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA.

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http://dx.doi.org/10.1002/jcc.1153DOI Listing
January 2002

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

J Org Chem 1996 May;61(11):3662-3668

Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143, and Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455.

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May 1996

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

J Comput Chem 1986 Apr;7(2):230-252

Department of Chemistry, University of California, Davis, California 95616.

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http://dx.doi.org/10.1002/jcc.540070216DOI Listing
April 1986