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Protein Science : a Publication of the Protein Society|November 27, 2020
Computational design of small molecular modulators of protein-protein interactions with a novel thermodynamic cycle: Allosteric inhibitors of HIV-1 integraseQinfang Sun, Vijayan S K Ramaswamy, Ronald Levy, et al.Viruses|January 23, 2024
Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent ReorganizationQinfang Sun, Avik Biswas, Dmitry Lyumkis, et al.The Journal of Physical Chemistry. B|January 25, 2011
Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulationsWeihua Zheng, Emilio Gallicchio, Nanjie Deng, et al.Journal of Chemical Theory and Computation|May 13, 2021
Alchemical Transfer Approach to Absolute Binding Free Energy EstimationJoe Z Wu, Solmaz Azimi, Sheenam Khuttan, et al.Journal of Computational Chemistry|December 24, 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 pointsRobert C Harris, Nanjie Deng, Ronald M Levy, et al.Biophysical Journal|September 3, 2020
Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein AssociationCeline Tse, Lauren Wickstrom, Mamuka Kvaratskhelia, et al.Journal of Computer-Aided Molecular Design|January 21, 2022
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challengeSolmaz Azimi, Joe Z Wu, Sheenam Khuttan, et al.Physical Chemistry Chemical Physics : PCCP|June 14, 2018
Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligandsNanjie Deng, Di Cui, Bin W Zhang, et al.Journal of the American Chemical Society|July 9, 2019
Indenoisoquinoline Topoisomerase Inhibitors Strongly Bind and Stabilize the MYC Promoter G-Quadruplex and Downregulate MYCKai-Bo Wang, Mohamed S A Elsayed, Guanhui Wu, et al.Viruses|June 2, 2021
Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid MutationQinfang Sun, Ronald M Levy, Karen A Kirby, et al.Pageof 4