Simulations of the Solution Structure of HIV-1 Protease in the Presence and Absence of Bound Zinc. - Darrin M. York; Lee J. Bartolotti; Thomas A. Darden; Lee G. Pedersen; M. W. Anderson (J. Comput. Chem., 1994)

Particle-Mesh Based Methods for Fast Ewald Summation in Molecular Dynamics Simulations. - Thomas A. Darden; Lee G. Pedersen; Abdulnour Y. Toukmaji; Michael F. Crowley; Thomas E. Cheatham (PP, 1997)

Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program. - Michael F. Crowley; Thomas A. Darden; Thomas E. Cheatham III; David W. Deerfield II (J. Supercomput., 1997)

A smooth-particle mesh Ewald method for DL_POLY molecular dynamics simulation package on the Fujitsu VPP700. - Kholmirzo Kholmurodov; William Smith; Kenji Yasuoka; Thomas A. Darden; Toshikazu Ebisuzaki (J. Comput. Chem., 2000)

Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method. - Leping Li; Clarice R. Weinberg; Thomas A. Darden; Lee G. Pedersen (Bioinform., 2001)

Predicted solution structure of zymogen human coagulation FVII. - Lalith E. Perera; Thomas A. Darden; Lee G. Pedersen (J. Comput. Chem., 2002)

The Amber biomolecular simulation programs. - David A. Case; Thomas E. Cheatham III; Tom Darden; Holger Gohlke; Ray Luo 001; Kenneth M. Merz Jr.; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J. Woods (J. Comput. Chem., 2005)

Gaussian induced dipole polarization model. - Dennis M. Elking; Tom Darden; Robert J. Woods (J. Comput. Chem., 2007)

Atomic forces for geometry-dependent point multipole and Gaussian multipole models. - Dennis M. Elking; Lalith E. Perera; Robert E. Duke; Thomas A. Darden; Lee G. Pedersen (J. Comput. Chem., 2010)

A finite field method for calculating molecular polarizability tensors for arbitrary multipole rank. - Dennis M. Elking; Lalith E. Perera; Robert E. Duke; Thomas A. Darden; Lee G. Pedersen (J. Comput. Chem., 2011)

Recent Developments in Amber Biomolecular Simulations. - David A. Case; David S. Cerutti; Vinícius Wilian D. Cruzeiro; Thomas A. Darden; Robert E. Duke; Mahdieh Ghazimirsaeed; George M. Giambasu; Timothy J. Giese; Andreas W. Götz; Julie A. Harris; Koushik Kasavajhala; Tai-Sung Lee; et al. (J. Chem. Inf. Model., 2025)