[1]K Vanommeslaeghe, E Hatcher, C Acharya, S Kundu, S Zhong, J Shim, E Darian, O Guvench, P Lopes, I Vorobyov, and Alexander D MacKerell Jr. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem., 31(4):671–690, March 2010.
[2]Kenno Vanommeslaeghe and Alexander D MacKerell Jr. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J. Chem. Inf. Model., 52(12):3144–3154, December 2012.
[3]Olgun Guvench and Alexander D MacKerell Jr. Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation. PLoS Comput. Biol., 5(7):e1000435–12, July 2009.
[4]Sirish Kaushik Lakkaraju, E Prabhu Raman, Wenbo Yu, and Alexander D MacKerell Jr. Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations. J. Chem. Theory Comput., 10(6):2281–2290, June 2014.
[5]E Prabhu Raman, Wenbo Yu, Sirish K Lakkaraju, and Alexander D MacKerell Jr. Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. J. Chem. Inf. Model., 53(12):3384–3398, December 2013.
[6]E Prabhu Raman, Kenno Vanommeslaeghe, and Alexander D MacKerell Jr. Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations. J. Chem. Theory Comput., 8(10):3513–3525, October 2012.
[7]E Prabhu Raman, Sirish Kaushik Lakkaraju, Rajiah Aldrin Denny, and Alexander D MacKerell Jr. 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. J. Comput. Chem., October 2016.
[8]E Prabhu Raman, Wenbo Yu, Olgun Guvench, and Alexander D MacKerell Jr. Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations. J. Chem. Inf. Model., 51(4):877–896, April 2011.
[9]Wenbo Yu, Sirish Kaushik Lakkaraju, E Prabhu Raman, Lei Fang, and Alexander D MacKerell Jr. Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules. J. Chem. Inf. Model., 55(2):407–420, February 2015.
[10]Sirish Kaushik Lakkaraju, Wenbo Yu, E Prabhu Raman, Alena V Hershfeld, Lei Fang, Deepak A Deshpande, and Alexander D MacKerell Jr. Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors. J. Chem. Inf. Model., 55(3):700–708, March 2015.