A framework for flexible and scalable replica-exchange on production distributed CI. - Brian K. Radak; Tai-Sung Lee; Peng He; Melissa Romanus; Ole Weidner; Wei Dai; Emilio Gallicchio; Nan-Jie Deng; Darrin M. York; Ronald M. Levy; Shantenu Jha (XSEDE, 2013)

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. - Emilio Gallicchio; Nan-Jie Deng; Peng He; Lauren Wickstrom; Alexander L. Perryman; Daniel N. Santiago; Stefano Forli; Arthur J. Olson; Ronald M. Levy (J. Comput. Aided Mol. Des., 2014)

Blind prediction of HIV integrase binding from the SAMPL4 challenge. - David L. Mobley; Shuai Liu; Nathan M. Lim; Karisa L. Wymer; Alexander L. Perryman; Stefano Forli; Nan-Jie Deng; Justin Su; Kim Branson; Arthur J. Olson (J. Comput. Aided Mol. Des., 2014)

Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. - Nan-Jie Deng; William F. Flynn; Junchao Xia; R. S. K. Vijayan; Baofeng Zhang; Peng He; Ahmet Mentes; Emilio Gallicchio; Ronald M. Levy (J. Comput. Aided Mol. Des., 2016)

Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points. - Robert C. Harris; Nan-Jie Deng; Ronald M. Levy; Ryosuke Ishizuka; Nobuyuki Matubayasi (J. Comput. Chem., 2017)

Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses. - Yoshitake Sakae; Bin W. Zhang; Ronald M. Levy; Nan-Jie Deng (J. Comput. Chem., 2020)

Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. - Qinfang Sun; Avik Biswas; R. S. K. Vijayan; Pierrick Craveur; Stefano Forli; Arthur J. Olson; Andres Emanuelli Castaner; Karen Kirby; Stefan G. Sarafianos; Nan-Jie Deng; Ronald M. Levy (J. Comput. Aided Mol. Des., 2022)