David A. Pearlman

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

David A. Pearlman, David A. Case, James W. Caldwell et al. · Computer Physics Communications · 1995 · 3.1K citations

Engineering, Normal Mode Analysis, Natural Sciences +13

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

Tai‐Sung Lee, Bryce K. Allen, Timothy J. Giese et al. · Journal of Chemical Information and Modeling · 2020 · 359 citations · Full text

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

Christophe Chipot, Richard L. Jaffe, Bernard Maigret et al. · Journal of the American Chemical Society · 1996 · 304 citations

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

Hege S. Beard, Anuradha Cholleti, David A. Pearlman et al. · PLoS ONE · 2013 · 275 citations · Full text

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

Kai Zhu, Tyler Day, Dora Toledo Warshaviak et al. · Proteins Structure Function and Bioinformatics · 2014 · 240 citations · Full text