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David A Pearlman
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Amber 10
DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ...
University of California, 2008
11930*2008
Amber 2021
DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ...
University of California, San Francisco, 2021
51082021
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and …
DA Pearlman, DA Case, JW Caldwell, WS Ross, TE Cheatham III, ...
Computer Physics Communications 91 (1-3), 1-41, 1995
37511995
AMBER 4.1
DA Pearlman, DA Case, JW Caldwell, WS Ross, TE Cheatham III, ...
University of California, San Francisco 45, 1995
7211995
AMBER11. University of California, San Francisco
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
Google Scholar There is no corresponding record for this reference, 2010
613*2010
Benzene dimer: A good model for π− π interactions in proteins? A comparison between the benzene and the toluene dimers in the gas phase and in an aqueous solution
C Chipot, R Jaffe, B Maigret, DA Pearlman, PA Kollman
Journal of the American Chemical Society 118 (45), 11217-11224, 1996
4111996
AMBER 5.0
DA Case, DA Pearlman, JW Caldwell, TE Cheatham III, WS Ross, ...
University of California, San Francisco, 1997
3421997
Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system
DA Pearlman, PS Charifson
Journal of medicinal chemistry 44 (21), 3417-3423, 2001
2762001
A comparison of alternative approaches to free energy calculations
DA Pearlman
The Journal of Physical Chemistry 98 (5), 1487-1493, 1994
2501994
Evaluating the molecular mechanics Poisson− Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase
DA Pearlman
Journal of medicinal chemistry 48 (24), 7796-7807, 2005
2382005
Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes
H Beard, A Cholleti, D Pearlman, W Sherman, KA Loving
PloS one 8 (12), e82849, 2013
2222013
Molecular models for DNA damaged by photoreaction
DA Pearlman, SR Holbrook, DH Pirkle, SH Kim
Science 227 (4692), 1304-1308, 1985
2211985
Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery
TS Lee, BK Allen, TJ Giese, Z Guo, P Li, C Lin, TD McGee Jr, ...
Journal of Chemical Information and Modeling 60 (11), 5595-5623, 2020
2052020
Antibody structure determination using a combination of homology modeling, energy‐based refinement, and loop prediction
K Zhu, T Day, D Warshaviak, C Murrett, R Friesner, D Pearlman
Proteins: Structure, Function, and Bioinformatics 82 (8), 1646-1655, 2014
2032014
The overlooked bond‐stretching contribution in free energy perturbation calculations
DA Pearlman, PA Kollman
The Journal of chemical physics 94 (6), 4532-4545, 1991
1831991
Are time-averaged restraints necessary for nuclear magnetic resonance refinement?: A model study for DNA
DA Pearlman, PA Kollman
Journal of molecular biology 220 (2), 457-479, 1991
1741991
The lag between the Hamiltonian and the system configuration in free energy perturbation calculations
DA Pearlman, PA Kollman
The Journal of chemical physics 91 (12), 7831-7839, 1989
1681989
San Francisco: University of California; 2004
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
AMBER10.[Google Scholar], 2004
1642004
CONCERTS:  Dynamic Connection of Fragments as an Approach to de Novo Ligand Design
DA Pearlman, MA Murcko
Journal of medicinal chemistry 39 (8), 1651-1663, 1996
1571996
A new method for carrying out free energy perturbation calculations: dynamically modified windows
DA Pearlman, PA Kollman
The Journal of chemical physics 90 (4), 2460-2470, 1989
1551989
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Articles 1–20