Yingkai Zhang

发表

Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S

Yuwei Yang, Jianing Lu, Chao Yang, 2019, Journal of Computer-Aided Molecular Design.

AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters

Joseph Katigbak, Haotian Li, Yingkai Zhang, 2020, J. Chem. Inf. Model..

Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions

Jianing Lu, Xuben Hou, Cheng Wang, 2019, J. Chem. Inf. Model..

Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning

Yingkai Zhang, Song Xia, Jianing Lu, 2021, J. Chem. Inf. Model..

Lin_F9: A Linear Empirical Scoring Function for Protein-Ligand Docking

Yingkai Zhang, Chao Yang, Yingkai Zhang, 2021, J. Chem. Inf. Model..

A pseudobond approach to combining quantum mechanical and molecular mechanical methods

Tai-Sung Lee, Yingkai Zhang, Weitao Yang, 1999 .

Studying the affinity and kinetics of molecular association with molecular-dynamics simulation

J. Andrew McCammon, Yingkai Zhang, J. Mccammon, 2003 .

Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation

Xuben Hou, Hao Fang, David Rooklin, 2016, Scientific Reports.

A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins.

Ruibo Wu, Zexing Cao, Yingkai Zhang, 2011, Journal of chemical theory and computation.

Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies.

Paul W Ayers, Qin Wu, Yingkai Zhang, 2009, The Journal of chemical physics.

An efficient linear scaling method for ab initio calculation of electron density of proteins

Yingkai Zhang, John Z. H. Zhang, J. H. Zhang, 2004 .

How does activation loop phosphorylation modulate catalytic activity in the cAMP‐dependent protein kinase: A theoretical study

J Andrew McCammon, Yingkai Zhang, Yuhui Cheng, 2006, Protein science : a publication of the Protein Society.

Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.

Yingkai Zhang, Shenglong Wang, Yingkai Zhang, 2007, The journal of physical chemistry. B.

Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.

Daiqian Xie, Yingkai Zhang, Shenglong Wang, 2009, The journal of physical chemistry. B.

Influence of Structural Fluctuation on Enzyme Reaction Energy Barriers in Combined Quantum Mechanical/Molecular Mechanical Studies

J. Andrew McCammon, Yingkai Zhang, J. Mccammon, 2003 .

An efficient approach for ab initio energy calculation of biopolymers.

John Z H Zhang, Yingkai Zhang, J. H. Zhang, 2005, The Journal of chemical physics.

Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study.

Ruibo Wu, Zexing Cao, Yingkai Zhang, 2010, Journal of chemical theory and computation.

Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions.

Yingkai Zhang, Zhenyu Lu, Yingkai Zhang, 2008, Journal of chemical theory and computation.

Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach.

J Andrew McCammon, Yingkai Zhang, J. Mccammon, 2002, Journal of the American Chemical Society.

Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study.

J Andrew McCammon, Yingkai Zhang, J. Mccammon, 2002, Journal of the American Chemical Society.

Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations.

Yingkai Zhang, Shenglong Wang, Yingkai Zhang, 2008, Journal of the American Chemical Society.

Ab initio QM/MM free-energy studies of arginine deiminase catalysis: the protonation state of the Cys nucleophile.

Hua Guo, Daiqian Xie, Yingkai Zhang, 2011, The journal of physical chemistry. B.

Molecular docking of balanol to dynamics snapshots of protein kinase A

J Andrew McCammon, Chung F Wong, Chung F. Wong, 2005, Proteins.

Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach

J Andrew McCammon, Yingkai Zhang, J. Mccammon, 2003, Protein science : a publication of the Protein Society.

Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods.

Yingkai Zhang, Yingkai Zhang, 2005, The Journal of chemical physics.

Revelation of a catalytic calcium-binding site elucidates unusual metal dependence of a human apyrase.

Min Lu, Yingkai Zhang, Yingkai Zhang, 2012, Journal of the American Chemical Society.

Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase.

Suse Broyde, Yingkai Zhang, S. Broyde, 2009, Journal of molecular biology.

Perspective on “Density-functional theory for fractional particle number: derivative discontinuities of the energy”

Yingkai Zhang, Weitao Yang, 2000 .

Comment on “Generalized Gradient Approximation Made Simple”

Yingkai Zhang, Weitao Yang, Weitao Yang, 1998 .

Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion

Suse Broyde, Yingkai Zhang, Shenglong Wang, 2012, Nucleic acids research.

A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.

Suse Broyde, Yingkai Zhang, S. Broyde, 2007, Journal of the American Chemical Society.

Describing van der Waals interaction in diatomic molecules with generalized gradient approximations: The role of the exchange functional

Yingkai Zhang, Weitao Yang, Weitao Yang, 1997 .

Pseudobond ab initio QM/MM approach and its applications to enzyme reactions

Yingkai Zhang, Yingkai Zhang, 2006 .

Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4.

Daiqian Xie, Yingkai Zhang, Shenglong Wang, 2009, The journal of physical chemistry. B.

Reaction mechanism of monoethanolamine with CO₂ in aqueous solution from molecular modeling.

Yingkai Zhang, Hong-Bin Xie, Yingkai Zhang, 2010, The journal of physical chemistry. A.

Determination of free energy profiles by repository based adaptive umbrella sampling: bridging nonequilibrium and quasiequilibrium simulations.

Yingkai Zhang, Han Zheng, 2008, The Journal of chemical physics.