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.


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.


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.


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.


Richard D Taylor, Malcolm MacCoss, and Alastair D G Lawson. Rings in drugs. J. Med. Chem., 57(14):5845–5859, July 2014.


Marc O’Reilly, Anne Cleasby, Thomas G Davies, Richard J Hall, R Frederick Ludlow, Christopher W Murray, Dominic Tisi, and Harren Jhoti. Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design. Drug Discov. Today, 24(5):1081–1086, May 2019.


Yang Zhang and Jeffrey Skolnick. SPICKER: a clustering approach to identify near-native protein folds. J. Comput. Chem., 25(6):865–871, April 2004.


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.


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.


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.


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.


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.


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.


Vincent D Ustach, Sirish Kaushik Lakkaraju, Sunhwan Jo, Wenbo Yu, Wenjuan Jiang, and Alexander D MacKerell Jr. Optimization and evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a tool for target-based ligand optimization. J. Chem. Inf. Model., 59(6):3018–3035, April 2019.


Geoffrey A Heinzl, Weiliang Huang, Wenbo Yu, Bennett J. Giardina, Yue Zhou, Alexander D MacKerell Jr, Angela Wilks, and Fengtian Xue. Iminoguanidines as Allosteric Inhibitors of the Iron-Regulated Heme Oxygenase (HemO) of Pseudomonas aeruginosa. J. Med. Chem., 59(14):6929–6942, June 2016.


Maryanna E Lanning, Wenbo Yu, Jeremy L Yap, Jay Chauhan, Lijia Chen, Ellis Whiting, Lakshmi S Pidugu, Tyler Atkinson, Hala Bailey, Willy Li, Braden M Roth, Lauren Hynicka, Kirsty Chesko, Eric A Toth, Paul Shapiro, Alexander D MacKerell Jr, Paul T Wilder, and Steven Fletcher. Structure-based design of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoates as selective inhibitors of the Mcl-1 oncoprotein. Eur. J. Med. Chem., 113:273–292, May 2016.