| Amber 10 DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... University of California, 2008 | 12499* | 2008 |
| Amber 2021 DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ... University of California, San Francisco, 2021 | 5845 | 2021 |
| 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 | 3826 | 1995 |
| AMBER 4.1 DA Pearlman, DA Case, JW Caldwell, WS Ross, TE Cheatham III, ... University of California, San Francisco 45, 1995 | 719 | 1995 |
| 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 | 415 | 1996 |
| 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 | 288 | 2001 |
| 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 | 266 | 2020 |
| A comparison of alternative approaches to free energy calculations DA Pearlman The Journal of Physical Chemistry 98 (5), 1487-1493, 1994 | 263 | 1994 |
| 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 | 248 | 2013 |
| 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 | 247 | 2005 |
| 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 | 225 | 2014 |
| Molecular models for DNA damaged by photoreaction DA Pearlman, SR Holbrook, DH Pirkle, SH Kim Science 227 (4692), 1304-1308, 1985 | 225 | 1985 |
| The overlooked bond‐stretching contribution in free energy perturbation calculations DA Pearlman, PA Kollman The Journal of chemical physics 94 (6), 4532-4545, 1991 | 178 | 1991 |
| 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 | 175 | 1991 |
| 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 | 170 | 1989 |
| San Francisco: University of California; 2008 DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ... AMBER8.[Google Scholar], 2004 | 163 | 2004 |
| 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 | 163 | 1996 |
| 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 | 159 | 2020 |
| 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 | 159 | 1998 |
| 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 | 154 | 1989 |
Thomas E. Cheatham, IIIProfessor of Medicinal Chemistry; Director Research Computing; University of UtahVerified email at utah.edu
