Automated Selection of Compounds with Physicochemical Properties To Maximize Bioavailability and Druglikeness. - Taiji Oashi; Ashley L. Ringer; E. Prabhu Raman; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2011)

Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations. - E. Prabhu Raman; Wenbo Yu 002; Olgun Guvench; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2011)

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges. - Kenno Vanommeslaeghe; E. Prabhu Raman; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2012)

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach. - E. Prabhu Raman; Wenbo Yu 002; Sirish Kaushik Lakkaraju; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2013)

Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. - Wenbo Yu 002; Sirish Kaushik Lakkaraju; E. Prabhu Raman; Alexander D. MacKerell Jr. (J. Comput. Aided Mol. Des., 2014)

Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors. - Sirish Kaushik Lakkaraju; Wenbo Yu 002; E. Prabhu Raman; Alena V. Hershfeld; Lei Fang; Deepak Deshpande; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2015)

Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules. - Wenbo Yu 002; Sirish Kaushik Lakkaraju; E. Prabhu Raman; Lei Fang; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2015)

Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches. - E. Prabhu Raman; Sirish Kaushik Lakkaraju; Rajiah Aldrin Denny; Alexander D. MacKerell Jr. (J. Comput. Chem., 2017)

Template-Based Method for Conformation Generation and Scoring for Congeneric Series of Ligands. - E. Prabhu Raman (J. Chem. Inf. Model., 2019)