Yingkai Zhang

Carmen Tse, Jun Xu, Liang Xu, Fu Kit Sheong, Shenglong Wang, Hoi Yee Chow, Xin Gao, Xuechen Li, Peter Cheung, Dong Wang, Yingkai Zhang, and Xuhui Huang, Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate, Nature Catalysis, 2, 228-235, 2019.

Jinping Lei, Gang Sheng, Peter Pak-Hang Cheung, Shenglong Wang, Yu Li, Xin Gao, Yingka  Zhang, Yanli Wang and Xuhui Huang, Two Symmetric Arginine Residues Play Distinct Roles in Thermus thermophilus Argonaute DNA Guide Strand-mediated DNA Target Cleavage, Proc. Natl. Acad. Sci., 116, 845-853, 2019.

Xuben Hou, David Rooklin, Duxiao Yang, Xiao Liang, Kangshuai Li, Jianing Lu, Cheng Wang, Peng Xiao, Yingkai Zhang, Jin-peng Sun, and Hao Fang, Computational strategy for bound state structure prediction in structure-based virtual screening: a case study of protein tyrosine phosphatase receptor type O inhibitors, J. Chem. Inf. Model. ,58, 2331-2342, 2018. (JCIM cover)

Hong Mu, Yingkai Zhang, Nicholas Geacintov, and Suse Broyde, Lesion sensing during initial binding by yeast XPC/Rad4: toward predicting resistance to nucleotide excision repair, Chem. Res. Toxicol., 31, 1260-1268, 2018. (ACS Editor’s Choice)

Linqiong Qiu, Jianing Song, Yingkai Zhang and John Zhang, Functional Loop Dynamics of the SComponent of ECF Transporter FolT, Molecular Physics, 116, 2613-2621, 2018.

Yuqin Cai, Iwen Fu, Nicholas Geacintov, Yingkai Zhang and Suse Broyde, Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition, DNA Repair, 65, 73-78, 2018.

David W. Rooklin, Ashley E Modell, Haotian Li, Viktoriya Berdan, Paramjit S. Arora, and Yingkai Zhang, Targeting Unoccupied Surfaces on Protein-Protein Interfaces, J. Am. Chem. Soc., 139, 15560-15563, 2017. (Communication, JACS cover)

Cheng Wang and Yingkai Zhang, Improving Scoring-Docking-Screening Powers of Protein-Ligand Scoring Functions using Random Forest, J. Comp. Chem., 28, 169-177, 2017.

Xuben Hou, David Rooklin, Hao Fang and Yingkai Zhang, Resveratrol Serves as a Protein-Substrate Interaction Stabilizer in Human SIRT1 Activation, Sci. Rep., 6, 38186, 2016.

Y. Zhou, S. Wang, Y. Li, and Y. Zhang, Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions, Methods in Enzymology: Computational approaches for studying Enzyme Mechanism, 577, 105-118, 2016 .

Hongwei Xu, Justin Diccianni, Joseph Katigbak, Chunhua Hu, Yingkai Zhang, and Tianning Diao, Bimetallic C–C Bond Forming Reductive Elimination from Nickel, J. Am. Chem. Soc., 138, 4779-4786, 2016.

Yanzi Zhou, Daiqian Xie, and Yingkai Zhang, Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides, J. Phys. Chem. Lett., 7, 1138-1142, 2016.

Iwen Fu, Yuqin Cai, Yuqin, Yingkai Zhang, Nicholas Geacintov, and Suse Broyde, Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study, Biochemistry, 55, 239-242, 2016. (Rapid Reports)

David W. Rooklin, Cheng Wang, Joseph Katigbak, Paramjit S. Arora, and Yingkai Zhang, AlphaSpace: Fragment-Centric Topographical Mapping to Target Protein-Protein Interaction Interfaces, J. Chem. Inf. Model. , 55, 1585-1599, 2015.

Wenjing Gong, Ruibo Wu and Yingkai Zhang, Thiol versus Hydroxamate as Zinc Binding Group in HDAC Inhibition: An ab initio QM/MM Molecular Dynamics Study, J. Comput. Chem., 36, 228 – 2235, 2015.

Hong Mu, Nicholas Geacintov, Yingkai Zhang, and Suse Broyde, Recognition of damaged DNA for nucleotide excision repair: a correlated motion mechanism with a mismatched cis-syn thymine dimer lesion, Biochemistry, 54, 5263 - 5267, 2015. (Accelerated Publication)

Jianping Lei, Yanzi Zhou, Daiqian Xie, and Yingkai Zhang, Mechanistic Insights into a Classic Wonder Drug – Aspirin, J. Am. Chem. Soc., 137, 70-73, 2015. (Communication)

Jingwei Zhou, Min Li, Nanhao Chen, Shenglong Wang, Hai-Bin Luo, Yingkai Zhang, and Ruibo Wu, Computational Design of a Time-Dependent Histone Deacetylase 2 Selective Inhibitor, ACS Chem. Biol., 10, 687-692, 2015. (Communication)

Nengjie Zhou, Qin Wu, and Yingkai Zhang, Force field development with density-based energy decomposition analysis, Chapter in `` Many-body effects and electrostatics in multi-scale computation of Biomolecules’’, Edited by Qiang Cui, Markus Meuwly and Pengyu Ren, 2015.

Xia Xiao , Neville R. Kallenbach , and Yingkai Zhang, Peptide Conformation Analysis using an Integrated Bayesian Approach, J. Chem. Theory Comput., 10, 4152-4159, 2014. http://dx.doi.org/10.1021/ct500433d

Lee Lior-Hoffmann, Shuang Ding, Nicholas E. Geacintov, Yingkai Zhang, and Suse Broyde, Structural and Dynamic Characterization of Polymerase κ’s Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity, Biochemistry, 53, 5683-5691, 2014. http://dx.doi.org/10.1021/bi5007964

Nengjie Zhou, Zhenyu Lu, Qin Wu, and Yingkai Zhang, Improved Parameterization of Interatomic Potentials for Rare Gas Dimers with Density-based Energy Decomposition Analysis, J. Chem.Phys., 140, 214117, 2014.

Gulseher Sirin and Yingkai Zhang, How is Acetylcholinesterase Phosphonylated by Soman? An ab initio QM/MM Molecular Dynamics Study, J. Phys. Chem. A, 118, 9132-9139, 2014.

Yuqin Cai, Han Zheng, Shuang Ding, Konstantin Kropachev, Adam G. Schwaid, Yijin Tang, Hong Mu, Shenglong Wang, Nicholas E. Geacintov, Yingkai Zhang, and Suse Broyde, Free Energy Profiles of Base Flipping in Intercalative Polycyclic Aromatic Hydrocarbon-Damaged DNA Duplexes: Energetic and Structural Relationships to Nucleotide Excision Repair Susceptibility, Chem. Res. Toxicol., 26, 1115–1125, 2013.

Jin Yang, Lee Lior-Hoffmann, Shenglong Wang, Yingkai Zhang, and Suse Broyde, DNA cytosine methylation: Structural and thermodynamic characterization of the epigenetic marking mechanism, Biochemistry, 52, 2828-2838, 2013.

Yawei Shi, Yanzi Zhou, Shenglong Wang, and Yingkai Zhang, Sirtuin Deacetylation Mechanism and Catalytic Role of the Dynamic Cofactor Binding Loop, J. Phys. Chem. Lett., 4, 491-495, 2013

Gulseher Sirin, Yanzi Zhou, Lee Lior-Hoffmann, Shenglong Wang, and Yingkai Zhang, Aging Mechanism of Soman Inhibited Acetylcholinesterase, J. Phys. Chem. B., 116, 12199-12207, 2012.

David Rooklin, Min Lu, and Yingkai Zhang, Revelation of a Catalytic Calcium-Binding Site Elucidates Unusual Metal Dependence of a Human Apyrase, J. Am. Chem. Soc., 134, 15595-15603, 2012. (Featured in JACS Spotlights, doi: 10.1021/ja309634z )

Lee Lior-Hoffmann, Lihua Wang, Shenglong Wang, Nicholas Geacintov, Suse Broyde and Yingkai Zhang, Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion, Nucleic Acids Res., 40, 9193-9205, 2012.