| AMBER 4.1 DA Case, JW Caldwell, WS Ross, TE Cheatham III, DM Ferguson, ... Department of Pharmaceutical Chemistry, University of California: San …, 1995 | 27828* | 1995 |
| PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data DR Roe, TE Cheatham III Journal of chemical theory and computation 9 (7), 3084-3095, 2013 | 6614 | 2013 |
| Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models PA Kollman, I Massova, C Reyes, B Kuhn, S Huo, L Chong, M Lee, T Lee, ... Accounts of chemical research 33 (12), 889-897, 2000 | 5287 | 2000 |
| 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 | 3833 | 1995 |
| Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations IS Joung, TE Cheatham III The journal of physical chemistry B 112 (30), 9020-9041, 2008 | 3607 | 2008 |
| Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers A Pérez, I Marchán, D Svozil, J Sponer, TE Cheatham, CA Laughton, ... Biophysical journal 92 (11), 3817-3829, 2007 | 2477 | 2007 |
| Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate− DNA helices J Srinivasan, TE Cheatham, P Cieplak, PA Kollman, DA Case Journal of the American Chemical Society 120 (37), 9401-9409, 1998 | 1962 | 1998 |
| A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. TE Cheatham 3rd, P Cieplak, PA Kollman Journal of biomolecular structure & dynamics 16 (4), 845, 1999 | 1116 | 1999 |
| Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles M Zgarbová, M Otyepka, J Sponer, A Mladek, P Banas, TE Cheatham III, ... Journal of chemical theory and computation 7 (9), 2886-2902, 2011 | 1067 | 2011 |
| Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins TEIII Cheatham, JL Miller, T Fox, TA Darden, PA Kollman Journal of the American Chemical Society 117 (14), 4193-4194, 1995 | 1026 | 1995 |
| Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms J Shao, SW Tanner, N Thompson, TE Cheatham Journal of chemical theory and computation 3 (6), 2312-2334, 2007 | 941 | 2007 |
| Encyclopedia of computational chemistry P von Ragué Schleyer, NL Allinger, T Clark, J Gasteiger, P Kollman, ... J. Wiley & Sons, 1998 | 825* | 1998 |
| AMBER 4.1 DA Pearlman, DA Case, JW Caldwell, WS Ross, TE Cheatham III, ... University of California, San Francisco 45, 1995 | 721 | 1995 |
| AmberTools DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ... Journal of chemical information and modeling 63 (20), 6183-6191, 2023 | 656 | 2023 |
| Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters IS Joung, TE Cheatham III The Journal of Physical Chemistry B 113 (40), 13279-13290, 2009 | 627 | 2009 |
| Refinement of the sugar–phosphate backbone torsion beta for AMBER force fields improves the description of Z-and B-DNA M Zgarbová, J Sponer, M Otyepka, TE Cheatham III, R Galindo-Murillo, ... Journal of chemical theory and computation 11 (12), 5723-5736, 2015 | 534 | 2015 |
| AMBER 14; University of California: San Francisco, 2014 DA Case, V Babin, JT Berryman, RM Betz, Q Cai, DS Cerutti, ... There is no corresponding record for this reference, 1-826, 2014 | 532* | 2014 |
| Assessing the current state of amber force field modifications for DNA R Galindo-Murillo, JC Robertson, M Zgarbova, J Sponer, M Otyepka, ... Journal of chemical theory and computation 12 (8), 4114-4127, 2016 | 490 | 2016 |
| The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition SC Harvey, RKZ Tan, TE Cheatham III Journal of computational chemistry 19 (7), 726-740, 1998 | 489 | 1998 |
| Molecular dynamics simulation of nucleic acids PA Kollman, TE Cheatham III Annu. Rev. Phys. Chem 51, 435-471, 2000 | 465* | 2000 |
