Physics-Based Scoring of Protein-Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening. - Niu Huang; Chakrapani Kalyanaraman; John J. Irwin; Matthew P. Jacobson (J. Chem. Inf. Model., 2006)

An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. - Chakrapani Kalyanaraman; Matthew P. Jacobson (J. Comput. Aided Mol. Des., 2007)

A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series. - Chaya Rapp; Chakrapani Kalyanaraman; Aviva Schiffmiller; Esther Leah Schoenbrun; Matthew P. Jacobson (J. Chem. Inf. Model., 2011)

Prediction of Substrates for Glutathione Transferases by Covalent Docking. - Guang Qiang Dong; Sara Calhoun; Hao Fan 002; Chakrapani Kalyanaraman; Megan C. Branch; Susan T. Mashiyama; Nir London; Matthew P. Jacobson; Patricia C. Babbitt; Brian K. Shoichet; Richard N. Armstrong; Andrej Sali (J. Chem. Inf. Model., 2014)