| Amber 2021 DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ... University of California, San Francisco, 2021 | 5164 | 2021 |
| GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features TS Lee, DS Cerutti, D Mermelstein, C Lin, S LeGrand, TJ Giese, ... Journal of chemical information and modeling 58 (10), 2043-2050, 2018 | 334 | 2018 |
| 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 | 218 | 2020 |
| AMBER 2018 TA Darden, RE Duke, D Ghoreishi, MK Gilson, H Gohlke, AW Goetz, ... University of California, San Francisco, 2018 | 173* | 2018 |
| AmberTools 16 DA Case, RM Betz, W Botello-Smith, DS Cerutti, TE Cheatham III, ... University of California, San Francisco, 2016 | 141 | 2016 |
| Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package DJ Mermelstein, C Lin, G Nelson, R Kretsch, JA McCammon, RC Walker Journal of computational chemistry 39 (19), 1354-1358, 2018 | 76 | 2018 |
| Fully integrated FPGA molecular dynamics simulations C Yang, T Geng, T Wang, R Patel, Q Xiong, A Sanaullah, C Wu, J Sheng, ... Proceedings of the International Conference for High Performance Computing …, 2019 | 53 | 2019 |
| Simulation of lipid bilayer self-assembly using all-atom lipid force fields ÅA Skjevik, BD Madej, CJ Dickson, C Lin, K Teigen, RC Walker, IR Gould Physical Chemistry Chemical Physics 18 (15), 10573-10584, 2016 | 53 | 2016 |
| Improved alchemical free energy calculations with optimized smoothstep softcore potentials TS Lee, Z Lin, BK Allen, C Lin, BK Radak, Y Tao, HC Tsai, W Sherman, ... Journal of chemical theory and computation 16 (9), 5512-5525, 2020 | 40 | 2020 |
| Simulating water exchange to buried binding sites IY Ben-Shalom, C Lin, T Kurtzman, RC Walker, MK Gilson Journal of chemical theory and computation 15 (4), 2684-2691, 2019 | 39 | 2019 |
| Amber 2018, Univ DA Case, IY Ben-Shalom, SR Brozell, DS Cerutti, TE Cheatham III, ... California, San Fr, 1-923, 2018 | 36 | 2018 |
| AMBER 20182018University of California DA Case, IY Ben-Shalom, SR Brozell, DS Cerutti, TE Cheatham III, ... San Francisco, 0 | 34 | |
| Amber 2020, 2020 DA Case, K Belfon, IY Ben-Shalom, SR Brozell, DS Cerutti, TEI Cheatham, ... Google Scholar There is no corresponding record for this reference, 2019 | 30 | 2019 |
| AMBER16 package DA Case, D Cerutti, T Cheateham, T Darden, R Duke, T Giese, H Gohlke, ... University of California: San Francisco, CA, USA, 2016 | 30 | 2016 |
| Accounting for the central role of interfacial water in protein–ligand binding free energy calculations IY Ben-Shalom, Z Lin, BK Radak, C Lin, W Sherman, MK Gilson Journal of chemical theory and computation 16 (12), 7883-7894, 2020 | 27 | 2020 |
| Amber 16 and AmberTools17 DA Case, DS Cerutti, TE Cheatham, TA Darden, RE Duke, TJ Giese, ... University of California, San Francisco, 2017 | 27 | 2017 |
| Kollman DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ... PA, AMBER 8, 2023 | 23 | 2023 |
| Molecular dynamics range-limited force evaluation optimized for FPGAs C Yang, T Geng, T Wang, C Lin, J Sheng, V Sachdeva, W Sherman, ... 2019 IEEE 30th International Conference on Application-specific Systems …, 2019 | 23 | 2019 |
| AMBER 20162016University of California DA Case, RM Betz, DS Cerutti, TE Cheatham III, TA Darden, RE Duke, ... San Francisco, 0 | 21 | |
| AMBER 2020 TA Darden, RE Duke, G Giambasu, MK Gilson, H Gohlke, AW Goetz, ... University of California: San Francisco, 2020 | 20 | 2020 |
