The Amber biomolecular simulation programs DA Case, TE Cheatham III, T Darden, H Gohlke, R Luo, KM Merz Jr, ... Journal of computational chemistry 26 (16), 1668-1688, 2005 | 10247 | 2005 |
ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB JA Maier, C Martinez, K Kasavajhala, L Wickstrom, KE Hauser, ... Journal of chemical theory and computation 11 (8), 3696-3713, 2015 | 8849 | 2015 |
Amber 11 DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... University of California, 2010 | 8530 | 2010 |
Comparison of multiple Amber force fields and development of improved protein backbone parameters V Hornak, R Abel, A Okur, B Strockbine, A Roitberg, C Simmerling Proteins: Structure, Function, and Bioinformatics 65 (3), 712-725, 2006 | 7412 | 2006 |
Amber 2021 DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ... University of California, San Francisco, 2021 | 5469 | 2021 |
AMBER 9 DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ... University of California, San Francisco 45, 2006 | 3669 | 2006 |
ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution C Tian, K Kasavajhala, KAA Belfon, L Raguette, H Huang, AN Migues, ... Journal of chemical theory and computation 16 (1), 528-552, 2019 | 1131 | 2019 |
All-atom structure prediction and folding simulations of a stable protein C Simmerling, B Strockbine, AE Roitberg Journal of the American Chemical Society 124 (38), 11258-11259, 2002 | 721 | 2002 |
AMBER 8, University of California, San Francisco DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... There is no corresponding record for this reference, 2004 | 609* | 2004 |
Amber 10 DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... University of California, 2008 | 534* | 2008 |
Improved generalized born solvent model parameters for protein simulations H Nguyen, DR Roe, C Simmerling Journal of chemical theory and computation 9 (4), 2020-2034, 2013 | 478 | 2013 |
Generalized Born model with a simple, robust molecular volume correction J Mongan, C Simmerling, JA McCammon, DA Case, A Onufriev Journal of chemical theory and computation 3 (1), 156-169, 2007 | 440 | 2007 |
HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations V Hornak, A Okur, RC Rizzo, C Simmerling Proceedings of the National Academy of Sciences 103 (4), 915-920, 2006 | 440 | 2006 |
AMBER 5.0 DA Case, DA Pearlman, JW Caldwell, TE Cheatham III, WS Ross, ... University of California, San Francisco, 1997 | 351 | 1997 |
Amber 14 DA Case, V Babin, J Berryman, RM Betz, Q Cai, DS Cerutti, ... University of California, 2014 | 342* | 2014 |
Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber T Luchko, S Gusarov, DR Roe, C Simmerling, DA Case, J Tuszynski, ... Journal of chemical theory and computation 6 (3), 607-624, 2010 | 289 | 2010 |
Evaluating the performance of the ff99SB force field based on NMR scalar coupling data L Wickstrom, A Okur, C Simmerling Biophysical journal 97 (3), 853-856, 2009 | 260 | 2009 |
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 | 246 | 2014 |
Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent H Nguyen, J Maier, H Huang, V Perrone, C Simmerling Journal of the American Chemical Society 136 (40), 13959-13962, 2014 | 241 | 2014 |
AmberTools DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ... Journal of chemical information and modeling 63 (20), 6183-6191, 2023 | 219 | 2023 |