| All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins † AD MacKerell Jr, D Bashford, M Bellott, RL Dunbrack Jr, JD Evanseck, ... The journal of physical chemistry B 102 (18), 3586-3616, 1998 | 15656 | 1998 |
| 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 | 8975 | 2009 |
| CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields K Vanommeslaeghe, E Hatcher, C Acharya, S Kundu, S Zhong, J Shim, ... Journal of computational chemistry 31 (4), 671-690, 2010 | 6732 | 2010 |
| CHARMM36m: an improved force field for folded and intrinsically disordered proteins J Huang, S Rauscher, G Nawrocki, T Ran, M Feig, BL De Groot, ... Nature methods 14 (1), 71-73, 2017 | 4840 | 2017 |
| Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles RB Best, X Zhu, J Shim, PEM Lopes, J Mittal, M Feig, AD MacKerell Jr Journal of chemical theory and computation 8 (9), 3257-3273, 2012 | 4285 | 2012 |
| Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types JB Klauda, RM Venable, JA Freites, JW O’Connor, DJ Tobias, ... The journal of physical chemistry B 114 (23), 7830-7843, 2010 | 4273 | 2010 |
| Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in … AD Mackerell Jr, M Feig, CL Brooks III Journal of computational chemistry 25 (11), 1400-1415, 2004 | 3838 | 2004 |
| CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data J Huang, AD MacKerell Jr Journal of computational chemistry 34 (25), 2135-2145, 2013 | 3327 | 2013 |
| CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field J Lee, X Cheng, S Jo, AD MacKerell, JB Klauda, W Im Biophysical journal 110 (3), 641a, 2016 | 3223 | 2016 |
| All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data N Foloppe, AD MacKerell, Jr Journal of computational chemistry 21 (2), 86-104, 2000 | 1929 | 2000 |
| Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing K Vanommeslaeghe, AD MacKerell Jr Journal of chemical information and modeling 52 (12), 3144-3154, 2012 | 1816 | 2012 |
| Empirical force fields for biological macromolecules: overview and issues AD MacKerell Jr Journal of computational chemistry 25 (13), 1584-1604, 2004 | 1656 | 2004 |
| Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges K Vanommeslaeghe, EP Raman, AD MacKerell Jr Journal of chemical information and modeling 52 (12), 3155-3168, 2012 | 1637 | 2012 |
| Development and current status of the CHARMM force field for nucleic acids AD MacKerell Jr, N Banavali, N Foloppe Biopolymers: original Research on biomolecules 56 (4), 257-265, 2000 | 1288 | 2000 |
| Improved treatment of the protein backbone in empirical force fields AD MacKerell Jr, M Feig, CL Brooks Journal of the American Chemical Society 126 (3), 698-699, 2004 | 1094 | 2004 |
| An all-atom empirical energy function for the simulation of nucleic acids AD MacKerell Jr, J Wiorkiewicz-Kuczera, M Karplus Journal of the American Chemical society 117 (48), 11946-11975, 1995 | 932 | 1995 |
| All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution AD MacKerell Jr, NK Banavali Journal of computational chemistry 21 (2), 105-120, 2000 | 918 | 2000 |
| Extension of the CHARMM general force field to sulfonyl‐containing compounds and its utility in biomolecular simulations W Yu, X He, K Vanommeslaeghe, AD MacKerell Jr Journal of computational chemistry 33 (31), 2451-2468, 2012 | 893 | 2012 |
| An improved empirical potential energy function for molecular simulations of phospholipids SE Feller, AD MacKerell The Journal of Physical Chemistry B 104 (31), 7510-7515, 2000 | 887 | 2000 |
| A simple polarizable model of water based on classical Drude oscillators G Lamoureux, AD MacKerell, B Roux The Journal of chemical physics 119 (10), 5185-5197, 2003 | 827 | 2003 |
Benoit RouxProfessor of Biochemistry, The university of ChicagoVerified email at uchicago.edu
