David A Pearlman
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AMBER 9
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
University of California, San Francisco 45, 2006
7005*2006
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
32751995
AMBER 12; University of California: San Francisco, 2012
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
There is no corresponding record for this reference.[Google Scholar], 1-826, 2010
998*2010
AMBER 4.1
DA Pearlman, DA Case, JW Caldwell, WS Ross, TE Cheatham III, ...
University of California, San Francisco 45, 1995
6381995
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
3631996
amber (University of California, San Francisco)
DA Case, DA Pearlman, JW Caldwell, TE Cheatham III, J Wang, WS Ross, ...
There is no corresponding record for this reference.[Google Scholar], 2006
263*2006
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
2292001
A comparison of alternative approaches to free energy calculations
DA Pearlman
The Journal of Physical Chemistry 98 (5), 1487-1493, 1994
2151994
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
2022005
Molecular models for DNA damaged by photoreaction
DA Pearlman, DH Pirkle, SH Kim
Science 227 (4692), 1304-1308, 1985
1981985
The overlooked bond‐stretching contribution in free energy perturbation calculations
DA Pearlman, PA Kollman
The Journal of chemical physics 94 (6), 4532-4545, 1991
1721991
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
1641991
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
1471989
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
1371989
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
1311998
AMBER, version 9
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
University of California: San Francisco, CA, 2006
1282006
Free energy calculations. The long and winding gilded road
C Chipot, DA Pearlman
Molecular Simulation 28 (1-2), 1-12, 2002
1282002
Simulation of the solvation free energies for methane, ethane, and propane and corresponding amino acid dipeptides: a critical test of the bond-PMF correction, a new set of …
Y Sun, D Spellmeyer, DA Pearlman, P Kollman
Journal of the American Chemical Society 114 (17), 6798-6801, 1992
1241992
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
1211996
Molecular Dynamics Potential of Mean Force Calculations: A Study of the Toluene− Ammonium π-Cation Interactions
C Chipot, B Maigret, DA Pearlman, PA Kollman
Journal of the American Chemical Society 118 (12), 2998-3005, 1996
1131996
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Artiklar 1–20