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Zhiyong Zhang - Publications

Affiliations: 
Biology USTC, Downingtown, PA, United States 
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43 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
2023 Jia Q, Zeng H, Li M, Tang J, Xiao N, Gao S, Li H, Zhang J, Zhang Z, Xie W. Binding asymmetry and conformational studies of the AtGSDA dimer. Computational and Structural Biotechnology Journal. 21: 5515-5522. PMID 38022696 DOI: 10.1016/j.csbj.2023.11.004  0.321
2022 Li J, Zhong F, Li M, Liu Y, Wang L, Liu M, Li F, Zhang J, Wu J, Shi Y, Zhang Z, Tu X, Ruan K, Gao J. Two Binding Sites of SARS-CoV-2 Macrodomain 3 Probed by Oxaprozin and Meclomen. Journal of Medicinal Chemistry. PMID 36356292 DOI: 10.1021/acs.jmedchem.2c01168  0.577
2021 Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, Abeliovich H, Abildgaard MH, Abudu YP, Acevedo-Arozena A, Adamopoulos IE, Adeli K, Adolph TE, Adornetto A, Aflaki E, ... ... Zhang Z, ... ... Zhang Z, ... ... Zhang Z, ... ... Zhang Z, ... ... Zhang Z, ... ... Zhang Z, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 1-382. PMID 33634751 DOI: 10.1080/15548627.2020.1797280  0.326
2020 Lv M, Gao J, Li M, Ma R, Li F, Liu Y, Liu M, Zhang J, Yao X, Wu J, Shi Y, Tang Y, Pan Y, Zhang ZY, Ruan K. Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1. The Journal of Physical Chemistry Letters. PMID 32885980 DOI: 10.1021/Acs.Jpclett.0C02039  0.656
2020 Peng J, Yuan C, Hua X, Zhang Z. Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures. Epigenetics & Chromatin. 13: 28. PMID 32664941 DOI: 10.1186/S13072-020-00351-X  0.676
2019 Zuo G, Chen ZP, Jiang YL, Zhu Z, Ding C, Zhang Z, Chen Y, Zhou CZ, Li Q. Structural insights into repression of the Pneumococcal fatty acid synthesis pathway by repressor FabT and co-repressor acyl-ACP. Febs Letters. PMID 31291684 DOI: 10.1002/1873-3468.13534  0.311
2019 Zhang J, Guo Q, Gao J, Xu C, Zhang B, Li M, She J, Shi Y, Zhang Z, Ruan K, Wu J. Structural insight into the unique dsDNA binding topology of the human ORC2 wing helix domain. The Febs Journal. PMID 30963726 DOI: 10.1111/Febs.14844  0.675
2019 Peng J, Yuan C, Ma R, Zhang Z. Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations using Bayesian Inference. Journal of Chemical Theory and Computation. PMID 30908042 DOI: 10.1021/Acs.Jctc.9B00062  0.706
2019 Ye C, Ding C, Ma R, Wang J, Zhang Z. Electrostatic Interactions Determine Entrance/Release order of Substrates in the Catalytic Cycle of Adenylate Kinase. Proteins. PMID 30615212 DOI: 10.1002/Prot.25655  0.372
2018 Xu D, Ma R, Zhang J, Liu Z, Wu B, Peng J, Zhai Y, Gong Q, Shi Y, Wu J, Wu Q, Zhang Z, Ruan K. Dynamic Nature of CTCF Tandem 11 Zinc Fingers in Multivalent Recognition of DNA as Revealed by NMR Spectroscopy. The Journal of Physical Chemistry Letters. PMID 29965776 DOI: 10.1021/Acs.Jpclett.8B01440  0.756
2017 Xu L, Wang L, Peng J, Li F, Wu L, Zhang B, Lv M, Zhang J, Gong Q, Zhang R, Zuo X, Zhang Z, Wu J, Tang Y, Shi Y. Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions. Structure (London, England : 1993). PMID 29107486 DOI: 10.1016/J.Str.2017.09.013  0.772
2017 Bao X, Liu H, Liu X, Ruan K, Zhang Y, Zhang Z, Hu Q, Liu Y, Akram S, Zhang J, Gong Q, Wang W, Yuan X, Li J, Zhao L, et al. Mitosis-specific acetylation tunes Ran effector binding for chromosome segregation. Journal of Molecular Cell Biology. PMID 29040603 DOI: 10.1093/Jmcb/Mjx045  0.596
2017 Wen B, Wang W, Zhang J, Gong Q, Shi Y, Wu J, Zhang Z. Structural and dynamic properties of the C-terminal region of the Escherichia coli RNA chaperone Hfq: integrative experimental and computational studies. Physical Chemistry Chemical Physics : Pccp. PMID 28752165 DOI: 10.1039/C7Cp01044C  0.623
2017 Cheng P, Peng J, Zhang Z. SAXS-Oriented Ensemble Refinement of Flexible Biomolecules. Biophysical Journal. 112: 1295-1301. PMID 28402873 DOI: 10.1016/J.Bpj.2017.02.024  0.738
2016 Peng J, Zhang Z. Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations. Scientific Reports. 6: 29360. PMID 27377017 DOI: 10.1038/Srep29360  0.704
2016 Dong J, Zhang Y, Zhang Z. pH dependence of ligand-induced human epidermal growth factor receptor activation investigated by molecular dynamics simulations. Journal of Molecular Modeling. 22: 131. PMID 27179806 DOI: 10.1007/S00894-016-3000-6  0.3
2016 Ling S, Wang W, Yu L, Peng J, Cai X, Xiong Y, Hayati Z, Zhang L, Zhang Z, Song L, Tian C. Structure of an E. coli integral membrane sulfurtransferase and its structural transition upon SCN(-) binding defined by EPR-based hybrid method. Scientific Reports. 6: 20025. PMID 26817826 DOI: 10.1038/Srep20025  0.724
2016 Deng X, Qin X, Chen L, Jia Q, Zhang Y, Zhang Z, Lei D, Ren G, Zhou Z, Wang Z, Li Q, Xie W. Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA synthetase (hGlyRS) during Catalysis. The Journal of Biological Chemistry. PMID 26797133 DOI: 10.1074/Jbc.M115.679126  0.318
2015 Jia N, Liu N, Cheng W, Jiang YL, Sun H, Chen LL, Peng J, Zhang Y, Ding YH, Zhang ZH, Wang X, Cai G, Wang J, Dong MQ, Zhang Z, et al. Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein. Embo Reports. PMID 26711430 DOI: 10.15252/Embr.201540851  0.712
2015 Hu HX, Jiang YL, Zhao MX, Cai K, Liu S, Wen B, Lv P, Zhang Y, Peng J, Zhong H, Yu HM, Ren YM, Zhang Z, Tian C, Wu Q, et al. Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation. Scientific Reports. 5: 16470. PMID 26576507 DOI: 10.1038/Srep16470  0.74
2015 Zhang Y, Wen B, Peng J, Zuo X, Gong Q, Zhang Z. Determining structural ensembles of flexible multi-domain proteins using small-angle X-ray scattering and molecular dynamics simulations. Protein & Cell. 6: 619-23. PMID 25944044 DOI: 10.1007/S13238-015-0162-4  0.717
2015 Chen P, Liu Z, Wang X, Peng J, Sun Q, Li J, Wang M, Niu L, Zhang Z, Cai G, Teng M, Li X. Crystal and EM structures of human phosphoribosyl pyrophosphate synthase I (PRS1) provide novel insights into the disease-associated mutations. Plos One. 10: e0120304. PMID 25781187 DOI: 10.1371/Journal.Pone.0120304  0.707
2015 Zhang Z. Systematic methods for defining coarse-grained maps in large biomolecules. Advances in Experimental Medicine and Biology. 827: 33-48. PMID 25387958 DOI: 10.1007/978-94-017-9245-5_4  0.374
2014 Peng J, Zhang Z. Simulating Large-Scale Conformational Changes of Proteins by Accelerating Collective Motions Obtained from Principal Component Analysis. Journal of Chemical Theory and Computation. 10: 3449-58. PMID 26588312 DOI: 10.1021/Ct5000988  0.699
2014 Wen B, Peng J, Zuo X, Gong Q, Zhang Z. Characterization of protein flexibility using small-angle x-ray scattering and amplified collective motion simulations. Biophysical Journal. 107: 956-64. PMID 25140431 DOI: 10.1016/J.Bpj.2014.07.005  0.718
2014 Zou Y, Shao Z, Peng J, Li F, Gong D, Wang C, Zuo X, Zhang Z, Wu J, Shi Y, Gong Q. Crystal structure of triple-BRCT-domain of ECT2 and insights into the binding characteristics to CYK-4. Febs Letters. 588: 2911-20. PMID 25068414 DOI: 10.1016/J.Febslet.2014.07.019  0.779
2014 Yang YH, Jiang YL, Zhang J, Wang L, Bai XH, Zhang SJ, Ren YM, Li N, Zhang YH, Zhang Z, Gong Q, Mei Y, Xue T, Zhang JR, Chen Y, et al. Structural insights into SraP-mediated Staphylococcus aureus adhesion to host cells. Plos Pathogens. 10: e1004169. PMID 24901708 DOI: 10.1371/Journal.Ppat.1004169  0.38
2014 Zhao D, Wang X, Peng J, Wang C, Li F, Sun Q, Zhang Y, Zhang J, Cai G, Zuo X, Wu J, Shi Y, Zhang Z, Gong Q. Structural investigation of the interaction between the tandem SH3 domains of c-Cbl-associated protein and vinculin. Journal of Structural Biology. 187: 194-205. PMID 24878663 DOI: 10.1016/J.Jsb.2014.05.009  0.793
2014 Wang C, Zhu Y, Caceres TB, Liu L, Peng J, Wang J, Chen J, Chen X, Zhang Z, Zuo X, Gong Q, Teng M, Hevel JM, Wu J, Shi Y. Structural determinants for the strict monomethylation activity by trypanosoma brucei protein arginine methyltransferase 7. Structure (London, England : 1993). 22: 756-68. PMID 24726341 DOI: 10.1016/J.Str.2014.03.003  0.754
2014 Wang J, Qin S, Li F, Li S, Zhang W, Peng J, Zhang Z, Gong Q, Wu J, Shi Y. Crystal structure of human BS69 Bromo-ZnF-PWWP reveals its role in H3K36me3 nucleosome binding. Cell Research. 24: 890-3. PMID 24675531 DOI: 10.1038/Cr.2014.38  0.752
2014 Wang C, Zhu Y, Chen J, Li X, Peng J, Chen J, Zou Y, Zhang Z, Jin H, Yang P, Wu J, Niu L, Gong Q, Teng M, Shi Y. Crystal structure of arginine methyltransferase 6 from Trypanosoma brucei. Plos One. 9: e87267. PMID 24498306 DOI: 10.1371/Journal.Pone.0087267  0.767
2014 Shao Z, Yan W, Peng J, Zuo X, Zou Y, Li F, Gong D, Ma R, Wu J, Shi Y, Zhang Z, Teng M, Li X, Gong Q. Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate. Nucleic Acids Research. 42: 509-25. PMID 24081582 DOI: 10.1093/Nar/Gkt869  0.76
2014 Zhao D, Wang C, Zhang J, Wu J, Shi Y, Zhang Z, Gong Q. solution structure of tandem SH3 domain of Sorbin and SH3 domain-containing protein 1 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Mox/Pdb  0.637
2013 Wen B, Shi Y, Zhang Z. Clustering multi-domain protein structures in the essential dynamics subspace Journal of Theoretical and Computational Chemistry. 12. DOI: 10.1142/S0219633613410083  0.643
2012 Wu B, Wang F, Zhang J, Zhang Z, Qin L, Peng J, Li F, Liu J, Lu G, Gong Q, Yao X, Wu J, Shi Y. Identification and structural basis for a novel interaction between Vav2 and Arap3. Journal of Structural Biology. 180: 84-95. PMID 22750419 DOI: 10.1016/J.Jsb.2012.06.011  0.781
2012 Shao Z, Li F, Sy SM, Yan W, Zhang Z, Gong D, Wen B, Huen MS, Gong Q, Wu J, Shi Y. Specific recognition of phosphorylated tail of H2AX by the tandem BRCT domains of MCPH1 revealed by complex structure. Journal of Structural Biology. 177: 459-68. PMID 22154951 DOI: 10.1016/J.Jsb.2011.11.022  0.67
2012 Qiu Y, Zhang W, Zhao C, Wang Y, Wang W, Zhang J, Zhang Z, Li G, Shi Y, Tu X, Wu J. Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA. The Biochemical Journal. 442: 527-38. PMID 22150589 DOI: 10.1042/Bj20111885  0.662
2011 Zhang Z, Wriggers W. Polymorphism of the epidermal growth factor receptor extracellular ligand binding domain: the dimer interface depends on domain stabilization. Biochemistry. 50: 2144-56. PMID 21275429 DOI: 10.1021/bi101843s  0.312
2006 Zhang Z, Boyle PC, Lu BY, Chang JY, Wriggers W. Entropic folding pathway of human epidermal growth factor explored by disulfide scrambling and amplified collective motion simulations. Biochemistry. 45: 15269-78. PMID 17176049 DOI: 10.1021/bi0615083  0.307
2003 Wang J, Zhang Z, Liu H, Shi Y. Quasiequilibrium unfolding thermodynamics of a small protein studied by molecular dynamics simulation with an explicit water model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 67: 061903. PMID 16241257 DOI: 10.1103/Physreve.67.061903  0.586
2003 Zhang Z, Shi Y, Liu H. Molecular dynamics simulations of peptides and proteins with amplified collective motions Biophysical Journal. 84: 3583-3593. PMID 12770868 DOI: 10.1016/S0006-3495(03)75090-5  0.609
2003 He J, Zhang Z, Shi Y, Liu H. Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions Journal of Chemical Physics. 119: 4005-4017. DOI: 10.1063/1.1591717  0.592
2001 Zhang Z, Zhu Y, Shi Y. Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue Biophysical Chemistry. 89: 145-162. PMID 11254208 DOI: 10.1016/S0301-4622(00)00227-1  0.574
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