An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs. - Robert J. Petrella; Ioan Andricioaei; Bernard R. Brooks; Martin Karplus (J. Comput. Chem., 2003)

Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation. - Robert J. Petrella; Martin Karplus (J. Comput. Chem., 2005)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

A versatile method for systematic conformational searches: Application to CheY. - Robert J. Petrella (J. Comput. Chem., 2011)