Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems T Darden, D York, L Pedersen The Journal of chemical physics 98 (12), 10089-10092, 1993 | 29783 | 1993 |
CHARMM: the biomolecular simulation program BR Brooks, CL Brooks III, AD Mackerell Jr, L Nilsson, RJ Petrella, B Roux, ... Journal of computational chemistry 30 (10), 1545-1614, 2009 | 8695 | 2009 |
Amber 2021 DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ... University of California, San Francisco, 2021 | 5292 | 2021 |
The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods DM York, TA Darden, LG Pedersen The Journal of chemical physics 99 (10), 8345-8348, 1993 | 829 | 1993 |
A smooth solvation potential based on the conductor-like screening model DM York, M Karplus The Journal of Physical Chemistry A 103 (50), 11060-11079, 1999 | 486 | 1999 |
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 | 349 | 2018 |
Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a … Y Yang, H Yu, D York, Q Cui, M Elstner The Journal of Physical Chemistry A 111 (42), 10861-10873, 2007 | 318 | 2007 |
An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations K Nam, J Gao, DM York Journal of Chemical Theory and Computation 1 (1), 2-13, 2005 | 313 | 2005 |
A chemical potential equalization method for molecular simulations DM York, W Yang The Journal of chemical physics 104 (1), 159-172, 1996 | 278 | 1996 |
Constant pH replica exchange molecular dynamics in explicit solvent using discrete protonation states: implementation, testing, and validation JM Swails, DM York, AE Roitberg Journal of chemical theory and computation 10 (3), 1341-1352, 2014 | 265 | 2014 |
AMBER 2018, University of California, San Francisco, 2018 DA Case, JT Berryman, RM Betz, DS Cerutti, TE Cheatham III, TA Darden, ... Google Scholar There is no corresponding record for this reference, 2015 | 240 | 2015 |
Atomic-level accuracy in simulations of large protein crystals. DM York, A Wlodawer, LG Pedersen, TA Darden Proceedings of the National Academy of Sciences 91 (18), 8715-8718, 1994 | 239 | 1994 |
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 | 222 | 2020 |
Linear‐scaling semiempirical quantum calculations for macromolecules TS Lee, DM York, W Yang The Journal of Chemical Physics 105 (7), 2744-2750, 1996 | 222 | 1996 |
Toward the accurate modeling of DNA: the importance of long-range electrostatics DM York, W Yang, H Lee, T Darden, LG Pedersen Journal of the American Chemical Society 117 (17), 5001-5002, 1995 | 222 | 1995 |
Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms K Nam, Q Cui, J Gao, DM York Journal of Chemical Theory and Computation 3 (2), 486-504, 2007 | 174 | 2007 |
AmberTools DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ... Journal of chemical information and modeling 63 (20), 6183-6191, 2023 | 168 | 2023 |
Using AMBER18 for relative free energy calculations LF Song, TS Lee, C Zhu, DM York, KM Merz Jr Journal of chemical information and modeling 59 (7), 3128-3135, 2019 | 162 | 2019 |
Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis A Moser, K Range, DM York The Journal of Physical Chemistry B 114 (43), 13911-13921, 2010 | 162 | 2010 |
The fast Fourier Poisson method for calculating Ewald sums D York, W Yang The Journal of Chemical Physics 101 (4), 3298-3300, 1994 | 162 | 1994 |