Author

David A. Pearlman

Observed names: D A Pearlman, D. A. Pearlman, D. Pearlman, D.A. Pearlman, David A. Pearlman (6482546), David A. Pearlman A, David Pearlman, DavidA. Pearlman, David A. Pearlman

Observed institutions: Broad Institute, Centre National de la Recherche Scientifique, Lawrence Berkeley National Laboratory, University of California, San Francisco, Schrodinger (United States), University of California System, Stanley Center for Psychiatric Research, Université Henri Poincaré, Vertex Pharmaceuticals (United States), Massachusetts Institute of Technology, University of California, Berkeley

ORCID: 0000-0002-2574-6066

Observed ORCID: 0000-0002-2574-6066

OpenAlex ID: A5014464745

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

1995 · David A. Pearlman, David A. Case, et al. · Computer Physics Communications · 3,144

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

2020 · Tai-Sung Lee, Bryce K. Allen, et al. · Journal of Chemical Information and Modeling · 388

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

1996 · Christophe Chipot, Richard Jaffe, et al. · Journal of the American Chemical Society · 309

Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes

2013 · Hege Beard, Anuradha Cholleti, et al. · PLoS ONE · 267

Antibody structure determination using a combination of homology modeling, energy‐based refinement, and loop prediction

2014 · Kai Zhu, Tyler Day, et al. · Proteins Structure Function and Bioinformatics · 232

Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System

2001 · David A. Pearlman, Paul S. Charifson · Journal of Medicinal Chemistry · 221

A Comparison of Alternative Approaches to Free Energy Calculations

1994 · David A. Pearlman · The Journal of Physical Chemistry · 208

Rigorous Free Energy Simulations in Virtual Screening

2020 · Zoe Cournia, Bryce K. Allen, et al. · Journal of Chemical Information and Modeling · 201

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Evaluating the assumptions underlying force field development and application using free energy conformational maps for nucleosides

1991 · David A. Pearlman, Peter A. Kollman · Journal of the American Chemical Society · 195

Evaluating the Molecular Mechanics Poisson−Boltzmann Surface Area Free Energy Method Using a Congeneric Series of Ligands to p38 MAP Kinase

2005 · David A. Pearlman · Journal of Medicinal Chemistry · 192

Molecular Models for DNA Damaged by Photoreaction

1985 · David A. Pearlman, Stephen R. Holbrook, et al. · Science · 182

Ionic charging free energies: Spherical versus periodic boundary conditions

1998 · Tom Darden, David Pearlman, et al. · The Journal of Chemical Physics · 148

Are time-averaged restraints necessary for nuclear magnetic resonance refinement?

1991 · David A. Pearlman, Peter A. Kollman · Journal of Molecular Biology · 139

The overlooked bond-stretching contribution in free energy perturbation calculations

1991 · David A. Pearlman, Peter A. Kollman · The Journal of Chemical Physics · 135

The lag between the Hamiltonian and the system configuration in free energy perturbation calculations

1989 · David A. Pearlman, Peter A. Kollman · The Journal of Chemical Physics · 131

A new method for carrying out free energy perturbation calculations: Dynamically modified windows

1989 · David A. Pearlman, Peter A. Kollman · The Journal of Chemical Physics · 117

CONCERTS: Dynamic Connection of Fragments as an Approach to de Novo Ligand Design

1996 · David A. Pearlman, Mark A. Murcko · Journal of Medicinal Chemistry · 116

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 hydrocarbon parameters, and the gas phase-water hydrophobicity scale

1992 · Yaxiong Sun, David Spellmeyer, et al. · Journal of the American Chemical Society · 115

Structure-based approach to the prediction of disulfide bonds in proteins

2014 · Noeris K. Salam, Matvey Adzhigirey, et al. · Protein Engineering Design and Selection · 111

Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability—Large-Scale Validation of MD-Based Relative Free Energy Calculations

2016 · Thomas Steinbrecher, Chongkai Zhu, et al. · Journal of Molecular Biology · 109

Free Energy Calculations. The Long and Winding Gilded Road

2002 · Christophe Chipot, David A. Pearlman · Molecular Simulation · 98

CONCEPTS: New dynamic algorithm for de novo drug suggestion

1993 · David A. Pearlman, Mark A. Murcko · Journal of Computational Chemistry · 91

Improved Scoring of Ligand−Protein Interactions Using OWFEG Free Energy Grids

2001 · David A. Pearlman, Paul S. Charifson · Journal of Medicinal Chemistry · 89

Molecular Dynamics Potential of Mean Force Calculations: A Study of the Toluene−Ammonium π-Cation Interactions

1996 · Christophe Chipot, Bernard Maigret, et al. · Journal of the American Chemical Society · 83

Determining the contributions of constraints in free energy calculations: Development, characterization, and recommendations

1993 · David A. Pearlman · The Journal of Chemical Physics · 67

Works count: 72

Citation count: 8,106

H-index: 35

I10-index: 56