CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications.
Cerutti DS, Jain T, McCammon JA, Protein Sci, 2006 Jul - link

Molecular docking of balanol to dynamics snapshots of protein kinase A.
Wong CF, Kua J, Zhang Y, Straatsma TP, McCammon JA, Proteins, 2005 Dec 1 - link

Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach.
Kua J, Zhang Y, Eslami AC, Butler JR, McCammon JA, Protein Sci, 2003 Dec - link

Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach.
Kua J, Zhang Y, McCammon JA, J Am Chem Soc, 2002 Jul 17 - link

Situs: A package for docking crystal structures into low-resolution maps from electron microscopy.
Wriggers W, Milligan RA, McCammon JA, J Struct Biol, 1999 Apr-May - link

Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex.
Zacharias M, Luty BA, Davis ME, McCammon JA, J Mol Biol, 1994 May 6 - link