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Methods in Molecular Biology (Clifton, N.J.)|August 25, 2019
Using Molecular Dynamics Free Energy Simulation to Compute Binding Affinities of DNA G-Quadruplex LigandsNanjie DengThe Journal of Physical Chemistry. B|February 10, 2026
Toward Reconciling the Standard Binding Free Energy of Lenacapavir to HIV-1 Capsid with Experiment: Thermodynamic Effects of Solvent Buffer and Ligand ReorganizationQinfang Sun, Emilio Gallicchio, Ronald Levy, et al.Journal of Chemical Theory and Computation|August 4, 2015
Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energiesNanjie Deng, Bin W Zhang, Ronald M LevyJournal of Chemical Theory and Computation|February 27, 2020
Combining Alchemical Transformation with a Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding SitesJeffrey Cruz, Lauren Wickstrom, Danzhou Yang, et al.Journal of Chemical Theory and Computation|September 14, 2017
Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from EquilibriumBin W Zhang, Nanjie Deng, Zhiqiang Tan, et al.Biorxiv : the Preprint Server for Biology|December 11, 2023
Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganizationQinfang Sun, Avik Biswas, Dmitry Lyumkis, et al.Journal of Computational Chemistry|October 18, 2019
Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the PosesYoshitake Sakae, Bin W Zhang, Ronald M Levy, et al.Physical Chemistry Chemical Physics : PCCP|February 25, 2022
Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic modelLauren Wickstrom, Emilio Gallicchio, Lieyang Chen, et al.International Journal of Molecular Sciences|October 13, 2021
Evaluating Molecular Docking Software for Small Molecule Binding to G-Quadruplex DNAJonathan Dickerhoff, Kassandra R Warnecke, Kaibo Wang, et al.The Journal of Physical Chemistry. B|November 1, 2017
Resolving the Ligand-Binding Specificity in c-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR ExperimentNanjie Deng, Lauren Wickstrom, Piotr Cieplak, et al.Pageof 4