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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
12401*2008
Amber 2021
DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ...
University of California, San Francisco, 2021
54842021
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
37681995
AMBER 4.1
DA Pearlman, DA Case, JW Caldwell, WS Ross, TE Cheatham III, ...
University of California, San Francisco 45, 1995
7191995
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
4131996
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
2852001
A comparison of alternative approaches to free energy calculations
DA Pearlman
The Journal of Physical Chemistry 98 (5), 1487-1493, 1994
2571994
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
2442005
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
2322013
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
2292020
Molecular models for DNA damaged by photoreaction
DA Pearlman, SR Holbrook, DH Pirkle, SH Kim
Science 227 (4692), 1304-1308, 1985
2231985
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
2152014
The overlooked bond‐stretching contribution in free energy perturbation calculations
DA Pearlman, PA Kollman
The Journal of chemical physics 94 (6), 4532-4545, 1991
1781991
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
1751991
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
1661989
San Francisco: University of California; 2008
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
AMBER8.[Google Scholar], 2004
1632004
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
1581996
Ionic charging free energies: Spherical versus periodic boundary conditions
T Darden, D Pearlman, LG Pedersen
The Journal of chemical physics 109 (24), 10921-10935, 1998
1561998
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
1541989
Rigorous free energy simulations in virtual screening
Z Cournia, BK Allen, T Beuming, DA Pearlman, BK Radak, W Sherman
Journal of chemical information and modeling 60 (9), 4153-4169, 2020
1462020
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