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Journal of Chemical Information and Modeling|September 1, 2021
Lin_F9: A Linear Empirical Scoring Function for Protein-Ligand DockingChao Yang, Yingkai ZhangJournal of Chemical Theory and Computation|February 18, 2009
Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical ReactionsZhenyu Lu, Yingkai ZhangJournal of the American Chemical Society|January 26, 2006
Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structuresPo Hu, Yingkai ZhangThe Journal of Chemical Physics|June 3, 2008
Determination of free energy profiles by repository based adaptive umbrella sampling: bridging nonequilibrium and quasiequilibrium simulationsHan Zheng, Yingkai ZhangChemical Communications (Cambridge, England)|December 1, 2010
Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediateYanzi Zhou, Yingkai ZhangJournal of Chemical Information and Modeling|December 1, 2022
CovBinderInPDB: A Structure-Based Covalent Binder DatabaseXiao-Kang Guo, Yingkai ZhangJournal of Chemical Information and Modeling|April 1, 2025
Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds?Eric A Chen, Yingkai ZhangThe Journal of Physical Chemistry. A|May 3, 2014
How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics studyGulseher Sarah Sirin, Yingkai ZhangJournal of Computational Chemistry|April 29, 2009
Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulationsHan Zheng, Shenglong Wang, Yingkai ZhangJournal of Molecular Biology|April 25, 2009
Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymeraseLihua Wang, Suse Broyde, Yingkai ZhangPageof 768