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Yingkai Zhang, Ph.D. - Publications

Affiliations: 
Chemistry New York University, New York, NY, United States 
Area:
Enzyme simulations
Website:
http://www.nyu.edu/projects/yzhang/

78 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Lu J, Hou X, Wang C, Zhang Y. Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions. Journal of Chemical Information and Modeling. PMID 31638801 DOI: 10.1021/acs.jcim.9b00645  0.96
2019 Marsiglia WM, Katigbak J, Zheng S, Mohammadi M, Zhang Y, Traaseth NJ. A Conserved Allosteric Pathway in Tyrosine Kinase Regulation. Structure (London, England : 1993). PMID 31204250 DOI: 10.1016/j.str.2019.05.002  0.4
2019 Ka Man Tse C, Xu J, Xu L, Sheong FK, Wang S, Chow HY, Gao X, Li X, Cheung PP, Wang D, Zhang Y, Huang X. Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate. Nature Energy. 2: 228-235. PMID 31179024 DOI: 10.1038/s41929-019-0227-5  0.96
2019 Lu J, Wang C, Zhang Y. Predicting Molecular Energy using Force-Field Optimized Geometries and Atomic Vector Representations Learned from Improved Deep Tensor Neural Network. Journal of Chemical Theory and Computation. PMID 31142110 DOI: 10.1021/acs.jctc.9b00001  0.96
2019 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, et al. Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22. The Journal of Biological Chemistry. PMID 30979725 DOI: 10.1074/jbc.RA118.007129  0.92
2019 Li C, Sun N, Li L, Duan J, Zhang Y. Transposterior arch lateral mass screw for C1 fixation: Application of 3.5-mm-diameter screw in the vertebral artery groove with a height of ≤ 3.5 mm. World Neurosurgery. PMID 30922900 DOI: 10.1016/j.wneu.2019.03.175  0.64
2018 Lei J, Sheng G, Cheung PP, Wang S, Li Y, Gao X, Zhang Y, Wang Y, Huang X. Two symmetric arginine residues play distinct roles in Argonaute DNA guide strand-mediated DNA target cleavage. Proceedings of the National Academy of Sciences of the United States of America. PMID 30591565 DOI: 10.1073/pnas.1817041116  0.96
2018 Hou X, Rooklin DW, Yang D, Liang X, Li K, Lu J, Wang C, Xiao P, Zhang Y, Sun JP, Fang H. Computational strategy for bound state structure prediction in structure-based virtual screening: a case study of protein tyrosine phosphatase receptor type O inhibitors. Journal of Chemical Information and Modeling. PMID 30299094 DOI: 10.1021/acs.jcim.8b00548  0.96
2018 Mu H, Zhang Y, Geacintov NE, Broyde S. Lesion sensing during initial binding by yeast XPC/Rad4: toward predicting resistance to nucleotide excision repair. Chemical Research in Toxicology. PMID 30284444 DOI: 10.1021/acs.chemrestox.8b00231  0.64
2018 Cai Y, Fu I, Geacintov NE, Zhang Y, Broyde S. 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. PMID 29631253 DOI: 10.1016/j.dnarep.2018.02.009  0.64
2017 Rooklin D, Modell AE, Li H, Berdan V, Arora PS, Zhang Y. Targeting Unoccupied Surfaces on Protein-Protein Interfaces. Journal of the American Chemical Society. PMID 28759230 DOI: 10.1021/jacs.7b05960  0.64
2017 Mu H, Geacintov NE, Min JH, Zhang Y, Broyde S. The nucleotide excision repair lesion-recognition protein Rad4 captures a pre-flipped partner base in a benzo[a]pyrene-derived DNA lesion: how structure impacts the binding pathway. Chemical Research in Toxicology. PMID 28460163 DOI: 10.1021/acs.chemrestox.7b00074  0.64
2017 Chen C, Hou X, Wang G, Pan W, Yang X, Zhang Y, Fang H. Design, synthesis and biological evaluation of quinoline derivatives as HDAC class I inhibitors. European Journal of Medicinal Chemistry. 133: 11-23. PMID 28371677 DOI: 10.1016/j.ejmech.2017.03.064  0.84
2017 Fu I, Cai Y, Geacintov NE, Zhang Y, Broyde S. Nucleosome histone tail conformation and dynamics: impacts of lysine acetylation and a nearby minor groove benzo[a]pyrene-derived lesion. Biochemistry. PMID 28304160 DOI: 10.1021/acs.biochem.6b01208  0.64
2016 Hou X, Rooklin D, Fang H, Zhang Y. Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation. Scientific Reports. 6: 38186. PMID 27901083 DOI: 10.1038/srep38186  0.84
2016 Wang C, Zhang Y. Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. Journal of Computational Chemistry. PMID 27859414 DOI: 10.1002/jcc.24667  0.96
2016 Xu H, Diccianni JB, Katigbak J, Hu C, Zhang Y, Diao T. Bimetallic C-C Bond Forming Reductive Elimination from Nickel. Journal of the American Chemical Society. PMID 27005998 DOI: 10.1021/jacs.6b00016  1
2016 Zhou Y, Xie D, Zhang Y. Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides. The Journal of Physical Chemistry Letters. PMID 26958702 DOI: 10.1021/acs.jpclett.6b00373  1
2015 Fu I, Cai Y, Zhang Y, Geacintov NE, Broyde S. Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study. Biochemistry. PMID 26709619 DOI: 10.1021/acs.biochem.5b01166  0.64
2015 Gong W, Wu R, Zhang Y. Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An Ab initio QM/MM molecular dynamics study. Journal of Computational Chemistry. PMID 26452222 DOI: 10.1002/jcc.24203  1
2015 Mu H, Geacintov NE, Zhang Y, Broyde S. Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion. Biochemistry. 54: 5263-7. PMID 26270861 DOI: 10.1021/acs.biochem.5b00840  1
2015 Rooklin D, Wang C, Katigbak J, Arora PS, Zhang Y. AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein-Protein Interaction Interfaces. Journal of Chemical Information and Modeling. 55: 1585-99. PMID 26225450 DOI: 10.1021/acs.jcim.5b00103  1
2015 Zhou J, Li M, Chen N, Wang S, Luo HB, Zhang Y, Wu R. Computational design of a time-dependent histone deacetylase 2 selective inhibitor. Acs Chemical Biology. 10: 687-92. PMID 25546141 DOI: 10.1021/cb500767c  1
2015 Lei J, Zhou Y, Xie D, Zhang Y. Mechanistic insights into a classic wonder drug--aspirin. Journal of the American Chemical Society. 137: 70-3. PMID 25514511 DOI: 10.1021/ja5112964  0.88
2014 Xiao X, Kallenbach N, Zhang Y. Peptide Conformation Analysis Using an Integrated Bayesian Approach. Journal of Chemical Theory and Computation. 10: 4152-4159. PMID 25221447 DOI: 10.1021/ct500433d  1
2014 Lior-Hoffmann L, Ding S, Geacintov NE, Zhang Y, Broyde S. Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity. Biochemistry. 53: 5683-91. PMID 25148552 DOI: 10.1021/bi5007964  1
2014 Zhou N, Lu Z, Wu Q, Zhang Y. Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis. The Journal of Chemical Physics. 140: 214117. PMID 24908000 DOI: 10.1063/1.4881255  1
2014 Sirin GS, Zhang Y. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study. The Journal of Physical Chemistry. A. 118: 9132-9. PMID 24786171 DOI: 10.1021/jp502712d  1
2013 Cai Y, Zheng H, Ding S, Kropachev K, Schwaid AG, Tang Y, Mu H, Wang S, Geacintov NE, Zhang Y, Broyde S. Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: energetic and structural relationships to nucleotide excision repair susceptibility. Chemical Research in Toxicology. 26: 1115-25. PMID 23758590 DOI: 10.1021/tx400156a  1
2013 Shi Y, Zhou Y, Wang S, Zhang Y. Sirtuin Deacetylation Mechanism and Catalytic Role of the Dynamic Cofactor Binding Loop. The Journal of Physical Chemistry Letters. 4: 491-495. PMID 23585919 DOI: 10.1021/jz302015s  0.96
2013 Yang J, Lior-Hoffmann L, Wang S, Zhang Y, Broyde S. DNA cytosine methylation: structural and thermodynamic characterization of the epigenetic marking mechanism. Biochemistry. 52: 2828-38. PMID 23528166 DOI: 10.1021/bi400163k  1
2012 Sirin GS, Zhou Y, Lior-Hoffmann L, Wang S, Zhang Y. Aging mechanism of soman inhibited acetylcholinesterase. The Journal of Physical Chemistry. B. 116: 12199-207. PMID 22984913 DOI: 10.1021/jp307790v  1
2012 Rooklin DW, Lu M, Zhang Y. Revelation of a catalytic calcium-binding site elucidates unusual metal dependence of a human apyrase. Journal of the American Chemical Society. 134: 15595-603. PMID 22928549 DOI: 10.1021/ja307267y  1
2012 Lior-Hoffmann L, Wang L, Wang S, Geacintov NE, Broyde S, Zhang Y. 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 Research. 40: 9193-205. PMID 22772988 DOI: 10.1093/nar/gks653  1
2012 Zhou Y, Moin SM, Urban S, Zhang Y. An internal water-retention site in the rhomboid intramembrane protease GlpG ensures catalytic efficiency. Structure (London, England : 1993). 20: 1255-63. PMID 22705210 DOI: 10.1016/j.str.2012.04.022  0.88
2012 Wu R, Gong W, Liu T, Zhang Y, Cao Z. QM/MM molecular dynamics study of purine-specific nucleoside hydrolase. The Journal of Physical Chemistry. B. 116: 1984-91. PMID 22257300 DOI: 10.1021/jp211403j  1
2011 Lu Z, Zhou N, Wu Q, Zhang Y. Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development. Journal of Chemical Theory and Computation. 7: 4038-4049. PMID 22267958 DOI: 10.1021/ct2003226  1
2011 Ke Z, Smith GK, Zhang Y, Guo H. Molecular mechanism for eliminylation, a newly discovered post-translational modification. Journal of the American Chemical Society. 133: 11103-5. PMID 21710993 DOI: 10.1021/ja204378q  0.8
2011 Wu R, Lu Z, Cao Z, Zhang Y. A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins. Journal of Chemical Theory and Computation. 7: 433-443. PMID 21552372 DOI: 10.1021/ct100525r  1
2011 Wu R, Lu Z, Cao Z, Zhang Y. Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel. Journal of the American Chemical Society. 133: 6110-3. PMID 21456530 DOI: 10.1021/ja111104p  1
2011 Ke Z, Guo H, Xie D, Wang S, Zhang Y. Ab initio QM/MM free-energy studies of arginine deiminase catalysis: the protonation state of the Cys nucleophile. The Journal of Physical Chemistry. B. 115: 3725-33. PMID 21395290 DOI: 10.1021/jp200843s  0.96
2011 Zhou Y, Zhang Y. Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate. Chemical Communications (Cambridge, England). 47: 1577-9. PMID 21116528 DOI: 10.1039/c0cc04112b  0.88
2011 Shen J, Zhan C, Xie C, Meng Q, Gu B, Li C, Zhang Y, Lu W. Poly(ethylene glycol)-block-poly(D,L-lactide acid) micelles anchored with angiopep-2 for brain-targeting delivery. Journal of Drug Targeting. 19: 197-203. PMID 20446756 DOI: 10.3109/1061186X.2010.483517  0.64
2010 Zheng H, Cai Y, Ding S, Tang Y, Kropachev K, Zhou Y, Wang L, Wang S, Geacintov NE, Zhang Y, Broyde S. Base flipping free energy profiles for damaged and undamaged DNA. Chemical Research in Toxicology. 23: 1868-70. PMID 21090780 DOI: 10.1021/tx1003613  1
2010 Xie HB, Zhou Y, Zhang Y, Johnson JK. Reaction mechanism of monoethanolamine with CO₂ in aqueous solution from molecular modeling. The Journal of Physical Chemistry. A. 114: 11844-52. PMID 20939618 DOI: 10.1021/jp107516k  0.88
2010 Wu R, Wang S, Zhou N, Cao Z, Zhang Y. A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions. Journal of the American Chemical Society. 132: 9471-9. PMID 20568751 DOI: 10.1021/ja103932d  1
2010 Zhou Y, Wang S, Zhang Y. Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. The Journal of Physical Chemistry. B. 114: 8817-25. PMID 20550161 DOI: 10.1021/jp104258d  0.96
2009 Wu R, Hu P, Wang S, Cao Z, Zhang Y. Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study. Journal of Chemical Theory and Computation. 6: 337. PMID 20161624 DOI: 10.1021/ct9005322  1
2009 Ke Z, Wang S, Xie D, Zhang Y. Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4. The Journal of Physical Chemistry. B. 113: 16705-10. PMID 20028143 DOI: 10.1021/jp9080614  0.96
2009 Zheng H, Zhang Y. Introducing sampling entropy in repository based adaptive umbrella sampling. The Journal of Chemical Physics. 131: 214105. PMID 19968335 DOI: 10.1063/1.3267549  1
2009 Liu J, Zhang Y, Zhan CG. Reaction pathway and free-energy barrier for reactivation of dimethylphosphoryl-inhibited human acetylcholinesterase. The Journal of Physical Chemistry. B. 113: 16226-36. PMID 19924840 DOI: 10.1021/jp9055335  0.64
2009 Fahie K, Hu P, Swatkoski S, Cotter RJ, Zhang Y, Wolberger C. Side chain specificity of ADP-ribosylation by a sirtuin. The Febs Journal. 276: 7159-76. PMID 19895577 DOI: 10.1111/j.1742-4658.2009.07427.x  1
2009 Wu Q, Ayers PW, Zhang Y. Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies. The Journal of Chemical Physics. 131: 164112. PMID 19894932 DOI: 10.1063/1.3253797  1
2009 Ke Z, Zhou Y, Hu P, Wang S, Xie D, Zhang Y. Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. The Journal of Physical Chemistry. B. 113: 12750-8. PMID 19507815 DOI: 10.1021/jp903173c  1
2009 Zheng H, Wang S, Zhang Y. Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. Journal of Computational Chemistry. 30: 2706-11. PMID 19399770 DOI: 10.1002/jcc.21296  1
2009 Wang L, Broyde S, Zhang Y. Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase. Journal of Molecular Biology. 389: 787-96. PMID 19389406 DOI: 10.1016/j.jmb.2009.04.029  1
2008 Lu Z, Zhang Y. Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions. Journal of Chemical Theory and Computation. 4: 1237-48. PMID 19221605  1
2008 Hu P, Wang S, Zhang Y. Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations. Journal of the American Chemical Society. 130: 16721-8. PMID 19049465 DOI: 10.1021/ja807269j  1
2008 Zheng H, Zhang Y. Determination of free energy profiles by repository based adaptive umbrella sampling: bridging nonequilibrium and quasiequilibrium simulations. The Journal of Chemical Physics. 128: 204106. PMID 18513009 DOI: 10.1063/1.2920476  1
2008 Hu P, Wang S, Zhang Y. How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations. Journal of the American Chemical Society. 130: 3806-13. PMID 18311969 DOI: 10.1021/ja075896n  1
2007 Liu Z, Young AW, Hu P, Rice AJ, Zhou C, Zhang Y, Kallenbach NR. Tuning the membrane selectivity of antimicrobial peptides by using multivalent design. Chembiochem : a European Journal of Chemical Biology. 8: 2063-5. PMID 17924379 DOI: 10.1002/cbic.200700502  1
2007 Xiao C, Zhang Y. Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons. The Journal of Chemical Physics. 127: 124102. PMID 17902888 DOI: 10.1063/1.2774980  1
2007 Xiao C, Zhang Y. Catalytic mechanism and metal specificity of bacterial peptide deformylase: a density functional theory QM/MM study. The Journal of Physical Chemistry. B. 111: 6229-35. PMID 17503802 DOI: 10.1021/jp068657f  0.6
2007 Wang S, Hu P, Zhang Y. Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9. The Journal of Physical Chemistry. B. 111: 3758-64. PMID 17388541 DOI: 10.1021/jp067147i  1
2007 Wang L, Yu X, Hu P, Broyde S, Zhang Y. A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV. Journal of the American Chemical Society. 129: 4731-7. PMID 17375926 DOI: 10.1021/ja068821c  1
2006 Zhang C, Liang G, Zhang Y, Hu Y. [Response to dynamic strain in human periosteal cells grown in vitro]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi = Journal of Biomedical Engineering = Shengwu Yixue Gongchengxue Zazhi. 23: 546-50. PMID 16856386  0.56
2006 Corminboeuf C, Hu P, Tuckerman ME, Zhang Y. Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein Journal of the American Chemical Society. 128: 4530-4531. PMID 16594663 DOI: 10.1021/ja0600882  1
2006 Cheng Y, Zhang Y, McCammon JA. How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study. Protein Science : a Publication of the Protein Society. 15: 672-83. PMID 16522793 DOI: 10.1110/ps.051852306  1
2006 Karambelkar VV, Xiao C, Zhang Y, Sarjeant AA, Goldberg DP. Geometric preferences in iron(II) and zinc(II) model complexes of peptide deformylase. Inorganic Chemistry. 45: 1409-11. PMID 16471944 DOI: 10.1021/ic050995s  1
2006 Hu P, Zhang Y. Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures. Journal of the American Chemical Society. 128: 1272-8. PMID 16433545 DOI: 10.1021/ja056153+  1
2005 Wong CF, Kua J, Zhang Y, Straatsma TP, McCammon JA. Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins. 61: 850-8. PMID 16245317 DOI: 10.1002/prot.20688  1
2005 Chen X, Zhang Y, Zhang JZ. An efficient approach for ab initio energy calculation of biopolymers. The Journal of Chemical Physics. 122: 184105. PMID 15918692 DOI: 10.1063/1.1897382  0.56
2005 Cheng Y, Zhang Y, McCammon JA. How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study. Journal of the American Chemical Society. 127: 1553-62. PMID 15686389 DOI: 10.1021/ja0464084  1
2005 Zhang Y. Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods. The Journal of Chemical Physics. 122: 024114. PMID 15638579 DOI: 10.1063/1.1834899  1
2003 Kua J, Zhang Y, Eslami AC, Butler JR, McCammon JA. Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach. Protein Science : a Publication of the Protein Society. 12: 2675-84. PMID 14627729 DOI: 10.1110/ps.03318603  1
2003 Cisneros GA, Liu H, Zhang Y, Yang W. Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase. Journal of the American Chemical Society. 125: 10384-93. PMID 12926963 DOI: 10.1021/ja029672a  1
2002 Zhang Y, Kua J, McCammon JA. Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. Journal of the American Chemical Society. 124: 10572-7. PMID 12197759  1
2002 Kua J, Zhang Y, McCammon JA. Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach. Journal of the American Chemical Society. 124: 8260-7. PMID 12105904  1
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