Amber 2023 DA Case, HM Aktulga, K Belfon, IY Ben-Shalom, JT Berryman, SR Brozell, ... University of California, San Francisco, 2023 | 6256 | 2023 |
OPLS3: a force field providing broad coverage of drug-like small molecules and proteins E Harder, W Damm, J Maple, C Wu, M Reboul, JY Xiang, L Wang, ... Journal of chemical theory and computation 12 (1), 281-296, 2016 | 3092 | 2016 |
AmberTools DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ... Journal of chemical information and modeling 63 (20), 6183-6191, 2023 | 584 | 2023 |
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 | 396 | 2018 |
The FF14SB force field DA Case, V Babin, JT Berryman, RM Betz, Q Cai, DS Cerutti, ... Amber 14, 29-31, 2014 | 254 | 2014 |
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 | 248 | 2014 |
Further along the road less traveled: AMBER ff15ipq, an original protein force field built on a self-consistent physical model KT Debiec, DS Cerutti, LR Baker, AM Gronenborn, DA Case, LT Chong Journal of chemical theory and computation 12 (8), 3926-3947, 2016 | 205 | 2016 |
Staggered mesh Ewald: an extension of the smooth particle-mesh Ewald method adding great versatility DS Cerutti, RE Duke, TA Darden, TP Lybrand Journal of chemical theory and computation 5 (9), 2322-2338, 2009 | 161 | 2009 |
Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization DS Cerutti, JE Rice, WC Swope, DA Case The Journal of Physical Chemistry B 117 (8), 2328-2338, 2013 | 141 | 2013 |
AMBER 2018; 2018 DA Case, IY Ben-Shalom, SR Brozell, DS Cerutti, TE Cheatham III, ... University of California, San Francisco, 2018 | 130 | 2018 |
AmberTools 16 DA Case, RM Betz, W Botello-Smith, DS Cerutti, TE Cheatham III, ... University of California, San Francisco, 2016 | 126 | 2016 |
AMBER 14. 2014 DA Case, V Babin, J Berryman, RM Betz, Q Cai, DS Cerutti, ... University of California, San Francisco, 2014 | 113 | 2014 |
Amber 2020: University of california DA Case, K Belfon, I Ben-Shalom, S Brozell, D Cerutti, T Cheatham, ... San Francisco, 2020 | 111 | 2020 |
ff14ipq: A self-consistent force field for condensed-phase simulations of proteins DS Cerutti, WC Swope, JE Rice, DA Case Journal of chemical theory and computation 10 (10), 4515-4534, 2014 | 110 | 2014 |
Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models DS Cerutti, PL Freddolino, RE Duke Jr, DA Case The Journal of Physical Chemistry B 114 (40), 12811-12824, 2010 | 108 | 2010 |
Alchemical prediction of hydration free energies for SAMPL DL Mobley, S Liu, DS Cerutti, WC Swope, JE Rice Journal of computer-aided molecular design 26, 551-562, 2012 | 98 | 2012 |
A vulnerability in popular molecular dynamics packages concerning Langevin and Andersen dynamics DS Cerutti, R Duke, PL Freddolino, H Fan, TP Lybrand Journal of chemical theory and computation 4 (10), 1669-1680, 2008 | 94 | 2008 |
Simulations of a Protein Crystal: Explicit Treatment of Crystallization Conditions Links Theory and Experiment in the Streptavidin− Biotin Complex DS Cerutti, I Le Trong, RE Stenkamp, TP Lybrand Biochemistry 47 (46), 12065-12077, 2008 | 59 | 2008 |
Peptide crystal simulations reveal hidden dynamics PA Janowski, DS Cerutti, J Holton, DA Case Journal of the American Chemical Society 135 (21), 7938-7948, 2013 | 52 | 2013 |
Dynamics of the streptavidin− biotin complex in solution and in its crystal lattice: Distinct behavior revealed by molecular simulations DS Cerutti, IL Trong, RE Stenkamp, TP Lybrand The Journal of Physical Chemistry B 113 (19), 6971-6985, 2009 | 52 | 2009 |