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Thomas A Darden
Thomas A Darden
Other namesTom Darden
Senior Scientist OpenEye Cadence Molecular Sciences
Verified email at eyesopen.com
Title
Cited by
Cited by
Year
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
293541993
A smooth particle mesh Ewald method
U Essmann, L Perera, ML Berkowitz, T Darden, H Lee, LG Pedersen
The Journal of chemical physics 103 (19), 8577-8593, 1995
216341995
The Amber biomolecular simulation programs
DA Case, TE Cheatham III, T Darden, H Gohlke, R Luo, KM Merz Jr, ...
Journal of computational chemistry 26 (16), 1668-1688, 2005
95692005
Amber 10
DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ...
University of California, 2008
88092008
Amber 2021
DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ...
University of California, San Francisco, 2021
53512021
AMBER 9
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
University of California, San Francisco 45, 2006
34722006
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
1080*1993
Making optimal use of empirical energy functions: force‐field parameterization in crystal space
E Krieger, T Darden, SB Nabuurs, A Finkelstein, G Vriend
Proteins: Structure, Function, and Bioinformatics 57 (4), 678-683, 2004
9902004
Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins
TEIII Cheatham, JL Miller, T Fox, TA Darden, PA Kollman
Journal of the American Chemical Society 117 (14), 4193-4194, 1995
9891995
Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method
L Li, CR Weinberg, TA Darden, LG Pedersen
Bioinformatics 17 (12), 1131-1142, 2001
8502001
Molecular dynamics simulations of biomolecules: long-range electrostatic effects
C Sagui, TA Darden
Annual review of biophysics and biomolecular structure 28 (1), 155-179, 1999
7751999
New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations
T Darden, L Perera, L Li, L Pedersen
Structure 7 (3), R55-R60, 1999
7221999
AMBER 10; University of California: San Francisco, 2008
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
Google Scholar There is no corresponding record for this reference, 2008
5282008
Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions
A Toukmaji, C Sagui, J Board, T Darden
The Journal of chemical physics 113 (24), 10913-10927, 2000
4972000
AMBER 9; University of California: San Francisco, 2006
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
Google Scholar There is no corresponding record for this reference, 9-174, 2014
4952014
Anisotropic, polarizable molecular mechanics studies of inter-and intramolecular interactions and ligand− macromolecule complexes. A bottom-up strategy
N Gresh, GA Cisneros, TA Darden, JP Piquemal
Journal of chemical theory and computation 3 (6), 1960-1986, 2007
4042007
The coalescent process in models with selection
NL Kaplan, T Darden, RR Hudson
Genetics 120 (3), 819, 1988
3231988
AMBER11. University of California, San Francisco
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
Google Scholar There is no corresponding record for this reference, 2010
3132010
AMBER 14; University of California: San Francisco, 2014
DA Case, V Babin, JT Berryman, RM Betz, Q Cai, DS Cerutti, ...
Google Scholar There is no corresponding record for this reference, 1-826, 2014
305*2014
Simulation of Ca2+ and Mg2+ Solvation Using Polarizable Atomic Multipole Potential
D Jiao, C King, A Grossfield, TA Darden, P Ren
The journal of physical chemistry B 110 (37), 18553-18559, 2006
2882006
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Articles 1–20