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Yingkai Zhang

Professor of Chemistry

    1993 …2020

    Research output per year

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    Research Output

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    2020

    Inhibition of striatal-enriched protein tyrosine phosphatase by targeting computationally revealed cryptic pockets

    Hou, X., Sun, J. P., Ge, L., Liang, X., Li, K., Zhang, Y. & Fang, H., Mar 15 2020, In : European journal of medicinal chemistry. 190, 112131.

    Research output: Contribution to journalArticle

    Molecular basis for receptor tyrosine kinase A-loop tyrosine transphosphorylation

    Chen, L., Marsiglia, W. M., Chen, H., Katigbak, J., Erdjument-Bromage, H., Kemble, D. J., Fu, L., Ma, J., Sun, G., Zhang, Y., Liang, G., Neubert, T. A., Li, X., Traaseth, N. J. & Mohammadi, M., Mar 1 2020, In : Nature Chemical Biology. 16, 3, p. 267-277 11 p.

    Research output: Contribution to journalArticle

    Substrate interaction inhibits γ-secretase production of amyloid-β peptides

    Zhao, J., Xiao, Y., Liu, X., Kim, S., Wu, X., Barros, M., Zhuang, R., Hou, X., Zhang, Y., Robakis, N. K., Li, Y. M., Dordick, J. S., Ubarretxena-Belandia, I. & Wang, C., Feb 28 2020, In : Chemical Communications. 56, 17, p. 2578-2581 4 p.

    Research output: Contribution to journalArticle

    Open Access
    2019

    A Conserved Allosteric Pathway in Tyrosine Kinase Regulation

    Marsiglia, W. M., Katigbak, J., Zheng, S., Mohammadi, M., Zhang, Y. & Traaseth, N. J., Aug 6 2019, In : Structure. 27, 8, p. 1308-1315.e3

    Research output: Contribution to journalArticle

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

    Yang, Y., Lu, J., Yang, C. & Zhang, Y., Dec 1 2019, In : Journal of Computer-Aided Molecular Design. 33, 12, p. 1095-1105 11 p.

    Research output: Contribution to journalArticle

    Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22

    Li, K., Hou, X., Li, R., Bi, W., Yang, F., Chen, X., Xiao, P., Liu, T., Lu, T., Zhou, Y., Tian, Z., Shen, Y., Zhang, Y., Wang, J., Fang, H., Sun, J. & Yu, X., May 24 2019, In : Journal of Biological Chemistry. 294, 21, p. 8653-8663 11 p.

    Research output: Contribution to journalArticle

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

    Lu, J., Hou, X., Wang, C. & Zhang, Y., Nov 25 2019, In : Journal of Chemical Information and Modeling. 59, 11, p. 4540-4549 10 p.

    Research output: Contribution to journalArticle

    Intrinsic cleavage of RNA polymerase II adopts a nucleobase-independent mechanism assisted by transcript phosphate

    Tse, C. K. M., Xu, J., Xu, L., Sheong, F. K., Wang, S., Chow, H. Y., Gao, X., Li, X., Cheung, P. P. H., Wang, D., Zhang, Y. & Huang, X., Mar 1 2019, In : Nature Catalysis. 2, 3, p. 228-235 8 p.

    Research output: Contribution to journalArticle

    Two symmetric arginine residues play distinct roles in thermus thermophilus argonaute DNA guide strand-mediated DNA target cleavage

    Lei, J., Sheng, G., Cheung, P. P. H., Wang, S., Li, Y., Gao, X., Zhang, Y., Wang, Y. & Huang, X., Jan 15 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 3, p. 845-853 9 p.

    Research output: Contribution to journalArticle

    2018

    Computational Strategy for Bound State Structure Prediction in Structure-Based Virtual Screening: A Case Study of Protein Tyrosine Phosphatase Receptor Type O Inhibitors

    Hou, X., Rooklin, D., Yang, D., Liang, X., Li, K., Lu, J., Wang, C., Xiao, P., Zhang, Y., Sun, J. P. & Fang, H., Nov 26 2018, In : Journal of Chemical Information and Modeling. 58, 11, p. 2331-2342 12 p.

    Research output: Contribution to journalArticle

    Functional loop dynamics of the S-component of ECF transporter FolT

    Qiu, L., Shen, C., Song, J., Zhang, Y. & Zhang, J. Z. H., Oct 18 2018, In : Molecular Physics. 116, 19-20, p. 2613-2621 9 p.

    Research output: Contribution to journalArticle

    2017

    Design, synthesis and biological evaluation of quinoline derivatives as HDAC class I inhibitors

    Chen, C., Hou, X., Wang, G., Pan, W., Yang, X., Zhang, Y. & Fang, H., Jan 1 2017, In : European journal of medicinal chemistry. 133, p. 11-23 13 p.

    Research output: Contribution to journalArticle

    Improving scoring-docking-screening powers of protein–ligand scoring functions using random forest

    Wang, C. & Zhang, Y., Jan 30 2017, In : Journal of Computational Chemistry. 38, 3, p. 169-177 9 p.

    Research output: Contribution to journalArticle

    Targeting Unoccupied Surfaces on Protein-Protein Interfaces

    Rooklin, D., Modell, A. E., Li, H., Berdan, V., Arora, P. S. & Zhang, Y., Nov 8 2017, In : Journal of the American Chemical Society. 139, 44, p. 15560-15563 4 p.

    Research output: Contribution to journalArticle

    2016

    Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides

    Zhou, Y., Xie, D. & Zhang, Y., Apr 21 2016, In : Journal of Physical Chemistry Letters. 7, 7, p. 1138-1142 5 p.

    Research output: Contribution to journalArticle

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

    Hou, X., Rooklin, D., Fang, H. & Zhang, Y., Nov 30 2016, In : Scientific reports. 6, 38186.

    Research output: Contribution to journalArticle

    2015

    AlphaSpace: Fragment-Centric Topographical Mapping to Target Protein-Protein Interaction Interfaces

    Rooklin, D., Wang, C., Katigbak, J., Arora, P. S. & Zhang, Y., Aug 24 2015, In : Journal of Chemical Information and Modeling. 55, 8, p. 1585-1599 15 p.

    Research output: Contribution to journalArticle

    Computational design of a time-dependent histone deacetylase 2 selective inhibitor

    Zhou, J., Li, M., Chen, N., Wang, S., Luo, H. B., Zhang, Y. & Wu, R., Mar 20 2015, In : ACS Chemical Biology. 10, 3, p. 687-692 6 p.

    Research output: Contribution to journalArticle

    Mechanistic insights into a classic wonder drug-aspirin

    Lei, J., Zhou, Y., Xie, D. & Zhang, Y., Jan 14 2015, In : Journal of the American Chemical Society. 137, 1, p. 70-73 4 p.

    Research output: Contribution to journalArticle

    Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An Ab initio QM/MM molecular dynamics study

    Gong, W., Wu, R. & Zhang, Y., Nov 1 2015, In : Journal of Computational Chemistry. 36, 30, p. 2228-2235 8 p.

    Research output: Contribution to journalArticle

    2014

    How is acetylcholinesterase phosphonylated by Soman? An ab initio QM/MM molecular dynamics study

    Sirin, G. S. & Zhang, Y., Oct 2 2014, In : Journal of Physical Chemistry A. 118, 39, p. 9132-9139 8 p.

    Research output: Contribution to journalArticle

    Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis

    Zhou, N., Lu, Z., Wu, Q. & Zhang, Y., Jun 7 2014, In : Journal of Chemical Physics. 140, 21, 214117.

    Research output: Contribution to journalArticle

    Peptide conformation analysis using an integrated bayesian approach

    Xiao, X., Kallenbach, N. & Zhang, Y., Sep 9 2014, In : Journal of chemical theory and computation. 10, 9, p. 4152-4159 8 p.

    Research output: Contribution to journalArticle

    Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity

    Lior-Hoffmann, L., Ding, S., Geacintov, N. E., Zhang, Y. & Broyde, S., Sep 9 2014, In : Biochemistry. 53, 35, p. 5683-5691 9 p.

    Research output: Contribution to journalArticle

    2013

    DNA cytosine methylation: Structural and thermodynamic characterization of the epigenetic marking mechanism

    Yang, J., Lior-Hoffmann, L., Wang, S., Zhang, Y. & Broyde, S., Apr 23 2013, In : Biochemistry. 52, 16, p. 2828-2838 11 p.

    Research output: Contribution to journalArticle

    Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: Energetic and structural relationships to nucleotide excision repair susceptibility

    Cai, Y., Zheng, H., Ding, S., Kropachev, K., Schwaid, A. G., Tang, Y., Mu, H., Wang, S., Geacintov, N. E., Zhang, Y. & Broyde, S., Jul 15 2013, In : Chemical research in toxicology. 26, 7, p. 1115-1125 11 p.

    Research output: Contribution to journalArticle

    Sirtuin deacetylation mechanism and catalytic role of the dynamic cofactor binding loop

    Shi, Y., Zhou, Y., Wang, S. & Zhang, Y., Feb 7 2013, In : Journal of Physical Chemistry Letters. 4, 3, p. 491-495 5 p.

    Research output: Contribution to journalArticle

    2012

    Aging mechanism of soman inhibited acetylcholinesterase

    Sirin, G. S., Zhou, Y., Lior-Hoffmann, L., Wang, S. & Zhang, Y., Oct 11 2012, In : Journal of Physical Chemistry B. 116, 40, p. 12199-12207 9 p.

    Research output: Contribution to journalArticle

    An internal water-retention site in the rhomboid intramembrane protease GlpG ensures catalytic efficiency

    Zhou, Y., Moin, S. M., Urban, S. & Zhang, Y., Jul 3 2012, In : Structure. 20, 7, p. 1255-1263 9 p.

    Research output: Contribution to journalArticle

    Computational simulations of zinc enzyme: Challenges and recent advances

    Wu, R., Cao, Z. & Zhang, Y., Jun 1 2012, In : Progress in Chemistry. 24, 6, p. 1175-1184 10 p.

    Research output: Contribution to journalArticle

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

    Lior-Hoffmann, L., Wang, L., Wang, S., Geacintov, N. E., Broyde, S. & Zhang, Y., Oct 1 2012, In : Nucleic acids research. 40, 18, p. 9193-9205 13 p.

    Research output: Contribution to journalArticle

    QM/MM molecular dynamics study of purine-specific nucleoside hydrolase

    Wu, R., Gong, W., Liu, T., Zhang, Y. & Cao, Z., Feb 16 2012, In : Journal of Physical Chemistry B. 116, 6, p. 1984-1991 8 p.

    Research output: Contribution to journalArticle

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

    Rooklin, D. W., Lu, M. & Zhang, Y., Sep 19 2012, In : Journal of the American Chemical Society. 134, 37, p. 15595-15603 9 p.

    Research output: Contribution to journalArticle

    2011

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

    Ke, Z., Guo, H., Xie, D., Wang, S. & Zhang, Y., Apr 7 2011, In : Journal of Physical Chemistry B. 115, 13, p. 3725-3733 9 p.

    Research output: Contribution to journalArticle

    A transferable nonbonded pairwise force field to model zinc interactions in metalloproteins

    Wu, R., Lu, Z., Cao, Z. & Zhang, Y., Feb 8 2011, In : Journal of chemical theory and computation. 7, 2, p. 433-443 11 p.

    Research output: Contribution to journalArticle

    Directional dependence of hydrogen bonds: A density-based energy decomposition analysis and its implications on force field development

    Lu, Z., Zhou, N., Wu, Q. & Zhang, Y., Dec 13 2011, In : Journal of chemical theory and computation. 7, 12, p. 4038-4049 12 p.

    Research output: Contribution to journalArticle

    Molecular mechanism for eliminylation, a newly discovered post-translational modification

    Ke, Z., Smith, G. K., Zhang, Y. & Guo, H., Jul 27 2011, In : Journal of the American Chemical Society. 133, 29, p. 11103-11105 3 p.

    Research output: Contribution to journalArticle

    Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate

    Zhou, Y. & Zhang, Y., Feb 7 2011, In : Chemical Communications. 47, 5, p. 1577-1579 3 p.

    Research output: Contribution to journalArticle

    Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel

    Wu, R., Lu, Z., Cao, Z. & Zhang, Y., Apr 27 2011, In : Journal of the American Chemical Society. 133, 16, p. 6110-6113 4 p.

    Research output: Contribution to journalArticle

    2010

    A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions

    Wu, R., Wang, S., Zhou, N., Cao, Z. & Zhang, Y., Jul 14 2010, In : Journal of the American Chemical Society. 132, 27, p. 9471-9479 9 p.

    Research output: Contribution to journalArticle

    Base flipping free energy profiles for damaged and undamaged DNA

    Zheng, H., Cai, Y., Ding, S., Tang, Y., Kropachev, K., Zhou, Y., Wang, L., Wang, S., Geacintov, N. E., Zhang, Y. & Broyde, S., Dec 20 2010, In : Chemical research in toxicology. 23, 12, p. 1868-1870 3 p.

    Research output: Contribution to journalArticle

    Catalytic reaction mechanism of acetylcholinesterase determined by born-oppenheimer Ab initio QM/MM molecular dynamics simulations

    Zhou, Y., Wang, S. & Zhang, Y., Jul 8 2010, In : Journal of Physical Chemistry B. 114, 26, p. 8817-8825 9 p.

    Research output: Contribution to journalArticle

    Flexibility of catalytic zinc coordination in thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM molecular dynamics study

    Wu, R., Hu, P., Wang, S., Cao, Z. & Zhang, Y., Jan 12 2010, In : Journal of chemical theory and computation. 6, 1, p. 337-343 7 p.

    Research output: Contribution to journalArticle