| 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 | 27158 | 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 | 7826 | 2009 |
| AMBER 2015 DA Case, J Berryman, RM Betz, DS Cerutti, TE Cheatham Iii, TA Darden, ... University of California, 2015 | 3494 | 2015 |
| 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 | 868* | 1993 |
| Amber 2021 DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ... University of California, San Francisco, 2021 | 818 | 2021 |
| 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 | 440 | 1999 |
| 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 | 297 | 2005 |
| Amber 2015 (University of California, San Francisco) DA Case, IY Ben-Shalom, SR Brozell, DS Cerutti, TE Cheatham III, ... Available from ambermd. org/doc12/Amber15. pdf, 2015 | 295 | 2015 |
| 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 | 285 | 2007 |
| 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 | 279 | 2018 |
| A chemical potential equalization method for molecular simulations DM York, W Yang The Journal of chemical physics 104 (1), 159-172, 1996 | 264 | 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 | 240 | 2014 |
| 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 | 228 | 1994 |
| Linear‐scaling semiempirical quantum calculations for macromolecules TS Lee, DM York, W Yang The Journal of Chemical Physics 105 (7), 2744-2750, 1996 | 220 | 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 | 219 | 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 | 169 | 2007 |
| The fast Fourier Poisson method for calculating Ewald sums D York, W Yang The Journal of Chemical Physics 101 (4), 3298-3300, 1994 | 156 | 1994 |
| 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 | 148 | 2010 |
| 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 | 145 | 2020 |
| Solvent structure and hammerhead ribozyme catalysis M Martick, TS Lee, DM York, WG Scott Chemistry & biology 15 (4), 332-342, 2008 | 137 | 2008 |
Michael E HarrisProfessor of Chemistry, University of Florida在 chem.ufl.edu 的电子邮件经过验证
Michael E HarrisProfessor of Chemistry, University of Florida在 chem.ufl.edu 的电子邮件经过验证
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