Alexander D. MacKerell Jr.
Alexander D. MacKerell Jr.
Pharmaceutical Sciences, School of Pharmacy, University of Maryland
Verifierad e-postadress på rx.umaryland.edu - Startsida
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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
122851998
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
54032009
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
30142004
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
27802010
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
22252010
CHARMM: the energy function and its parameterization
AD MacKerell Jr, B Brooks, CL Brooks III, L Nilsson, B Roux, Y Won, ...
Encyclopedia of computational chemistry 1, 2002
1977*2002
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
19372012
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
15742000
Empirical force fields for biological macromolecules: overview and issues
AD MacKerell Jr
Journal of computational chemistry 25 (13), 1584-1604, 2004
12822004
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
9482000
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
8442013
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
8071995
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
7952004
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
7862000
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
7832000
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
6982012
A simple polarizable model of water based on classical Drude oscillators
G Lamoureux, AD MacKerell Jr, B Roux
The Journal of chemical physics 119 (10), 5185-5197, 2003
6732003
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
6672012
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
6622017
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
J Lee, X Cheng, JM Swails, MS Yeom, PK Eastman, JA Lemkul, S Wei, ...
Journal of chemical theory and computation 12 (1), 405-413, 2016
6072016
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