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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.

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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.

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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.

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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.

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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.

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