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Jun Zhang - Publications

Affiliations: 
2012-2017 College of Chemistry and Molecular Engineering Peking University, Beijing, Beijing Shi, China 
 2017- Department of Mathematics and Computer Science Freie Universität Berlin, Berlin, Germany 
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33 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 Zhang J, Liu S, Chen M, Chu H, Wang M, Wang Z, Yu J, Ni N, Yu F, Chen D, Yang YI, Xue B, Yang L, Liu Y, Gao YQ. Unsupervisedly Prompting AlphaFold2 for Accurate Few-Shot Protein Structure Prediction. Journal of Chemical Theory and Computation. PMID 37947474 DOI: 10.1021/acs.jctc.3c00528  0.527
2023 Huang Y, Zhang H, Jiang S, Yue D, Lin X, Zhang J, Gao YQ. DSDP: A Blind Docking Strategy Accelerated by GPUs. Journal of Chemical Information and Modeling. PMID 37386792 DOI: 10.1021/acs.jcim.3c00519  0.431
2023 Zhang J, Chen D, Xia Y, Huang YP, Lin X, Han X, Ni N, Wang Z, Yu F, Yang L, Yang YI, Gao YQ. Artificial Intelligence Enhanced Molecular Simulations. Journal of Chemical Theory and Computation. PMID 37358079 DOI: 10.1021/acs.jctc.3c00214  0.563
2023 Wang J, Xue Y, He Y, Quan H, Zhang J, Gao YQ. Characterization of network hierarchy reflects cell state specificity in genome organization. Genome Research. 33: 247-260. PMID 36828586 DOI: 10.1101/gr.277206.122  0.369
2022 Lei YK, Zhang Z, Han X, Yang YI, Zhang J, Gao YQ. Locating Transition Zone in Phase Space. Journal of Chemical Theory and Computation. PMID 36135927 DOI: 10.1021/acs.jctc.2c00385  0.565
2022 Li M, Zhang J, Niu H, Lei YK, Han X, Yang L, Ye Z, Yang YI, Gao YQ. Phase Transition between Crystalline Variants of Ordinary Ice. The Journal of Physical Chemistry Letters. 13: 8601-8606. PMID 36073968 DOI: 10.1021/acs.jpclett.2c02176  0.546
2022 Han X, Zhang J, Yang YI, Zhang Z, Yang L, Gao YQ. Enhanced Sampling Simulation Reveals How Solvent Influences Chirogenesis of the Intra-Molecular Diels-Alder Reaction. Journal of Chemical Theory and Computation. PMID 35666128 DOI: 10.1021/acs.jctc.2c00233  0.602
2021 Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C. DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes. Nature Communications. 12: 4108. PMID 34226550 DOI: 10.1038/s41467-021-24431-y  0.395
2021 Zhang J, Lei YK, Zhang Z, Han X, Li M, Yang L, Yang YI, Gao YQ. Deep reinforcement learning of transition states. Physical Chemistry Chemical Physics : Pccp. PMID 33729229 DOI: 10.1039/d0cp06184k  0.593
2020 Zhang J, Lei YK, Yang YI, Gao YQ. Deep learning for variational multiscale molecular modeling. The Journal of Chemical Physics. 153: 174115. PMID 33167648 DOI: 10.1063/5.0026836  0.597
2020 Zhang J, Lei YK, Zhang Z, Chang J, Li M, Han X, Yang L, Yang YI, Gao YQ. A Perspective on Deep Learning for Molecular Modeling and Simulations. The Journal of Physical Chemistry. A. PMID 32786668 DOI: 10.1021/acs.jpca.0c04473  0.571
2020 Zhang J, Lei YK, Zhang Z, Chang J, Li M, Han X, Yang L, Yang YI, Gao YQ. A Perspective on Deep Learning for Molecular Modeling and Simulations. The Journal of Physical Chemistry. B. PMID 32663004 DOI: 10.1021/acs.jpcb.0c04473  0.571
2019 Zhang J, Yang YI, Noé F. Targeted Adversarial Learning Optimized Sampling. The Journal of Physical Chemistry Letters. PMID 31522495 DOI: 10.1021/Acs.Jpclett.9B02173  0.638
2019 Zhang J, Lei YK, Che X, Zhang Z, Yang YI, Gao YQ. Deep Representation Learning for Complex Free-Energy Landscapes. The Journal of Physical Chemistry Letters. 5571-5576. PMID 31476868 DOI: 10.1021/acs.jpclett.9b02012  0.546
2019 Yang YI, Shao Q, Zhang J, Yang L, Gao YQ. Enhanced sampling in molecular dynamics. The Journal of Chemical Physics. 151: 070902. PMID 31438687 DOI: 10.1063/1.5109531  0.669
2019 Lei Y, Zhang J, Zhang Z, Gao Y. Dynamic Electric Field Complicates Chemical Reactions in Solutions. The Journal of Physical Chemistry Letters. PMID 31094529 DOI: 10.1021/acs.jpclett.9b01038  0.442
2019 Cai X, Xie WJ, Yang Y, Long Z, Zhang J, Qiao Z, Yang L, Gao YQ. Structure of water confined between two parallel graphene plates. The Journal of Chemical Physics. 150: 124703. PMID 30927866 DOI: 10.1063/1.5080788  0.381
2019 Dou JH, Yu ZA, Zhang J, Zheng YQ, Yao ZF, Tu Z, Wang X, Huang S, Liu C, Sun J, Yi Y, Cao X, Gao Y, Wang JY, Pei J. Organic Semiconducting Alloys with Tunable Energy Levels. Journal of the American Chemical Society. PMID 30810311 DOI: 10.1021/Jacs.8B13471  0.391
2018 Yi C, Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ. Unnatural cytosine bases recognized as thymines by DNA polymerases via the formation of the Watson-Crick geometry. Angewandte Chemie (International Ed. in English). PMID 30407705 DOI: 10.1002/anie.201807845  0.385
2018 Che X, Zhang J, Quan H, Yang L, Gao YQ. CDNs-STING Interaction Mechanism Investigations and Instructions on Design of CDN-Derivatives. The Journal of Physical Chemistry. B. PMID 29361230 DOI: 10.1021/acs.jpcb.7b12276  0.411
2017 Zhang J, Zhang Z, Yang YI, Liu S, Yang L, Gao YQ. Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories. Acs Central Science. 3: 407-414. PMID 28573202 DOI: 10.1021/acscentsci.7b00037  0.59
2017 Che X, Du XX, Cai X, Zhang J, Xie WJ, Long Z, Ye Z, Zhang H, Yang L, Su X, Gao YQ. Single Mutations Reshape the Structural Correlation Network of DMXAA-Human STING Complex. The Journal of Physical Chemistry. B. PMID 28178416 DOI: 10.1021/acs.jpcb.6b12472  0.382
2016 Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M, Stovicek O, Gao YQ, Yi C. Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair. Proceedings of the National Academy of Sciences of the United States of America. PMID 27354518 DOI: 10.1073/Pnas.1604591113  0.382
2016 Fu J, Yang YI, Zhang J, Chen Q, Shen X, Gao YQ. Structural Characteristics of Homogeneous Hydrophobic Ionic Liquid-HNO3-H2O Ternary System: Experimental Studies and Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 27196811 DOI: 10.1021/acs.jpcb.6b01214  0.544
2016 Yang YI, Zhang J, Che X, Yang L, Gao YQ. Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling. The Journal of Chemical Physics. 144: 094105. PMID 26957155 DOI: 10.1063/1.4943004  0.585
2016 Li X, Che X, Chen GH, Zhang J, Yan JL, Zhang YF, Zhang LS, Hsu CP, Gao YQ, Shi ZJ. Direct Oxidation of Aliphatic C-H Bonds in Amino-Containing Molecules under Transition-Metal-Free Conditions. Organic Letters. PMID 26949833 DOI: 10.1021/Acs.Orglett.5B03690  0.354
2016 Che X, Zhang J, Zhu Y, Yang L, Quan H, Gao YQ. Structural Flexibility and Conformation Features of Cyclic Dinucleotides in Aqueous Solutions. The Journal of Physical Chemistry. B. PMID 26878265 DOI: 10.1021/acs.jpcb.5b11531  0.399
2016 Duan Y, Gao Y, Zhang J, Chen Y, Jiang Y, Ji J, Zhang J, Chen X, Yang Q, Su L, Zhang J, Liu B, Zhu Z, Wang L, Yu Y. Mitochondrial aldehyde dehydrogenase 2 protects gastric mucosa cells against DNA damage caused by oxidative stress. Free Radical Biology & Medicine. PMID 26855420 DOI: 10.1016/j.freeradbiomed.2016.02.001  0.34
2015 Zhang J, Yang YI, Yang L, Gao YQ. Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories. The Journal of Physical Chemistry. B. PMID 26485567 DOI: 10.1021/acs.jpcb.5b08690  0.595
2015 Gu C, Zhang J, Yang YI, Chen X, Ge H, Sun Y, Su X, Yang L, Xie XS, Gao YQ. DNA Structural Correlation in Short and Long Ranges. The Journal of Physical Chemistry. B. PMID 26439165 DOI: 10.1021/Acs.Jpcb.5B06217  0.542
2015 Zhang J, Yang YI, Yang L, Gao YQ. Conformational Preadjustment in Aqueous Claisen Rearrangement Revealed by SITS-QM/MM MD Simulations. The Journal of Physical Chemistry. B. 119: 5518-30. PMID 25849201 DOI: 10.1021/jp511057f  0.593
2015 Yang L, Liu CW, Shao Q, Zhang J, Gao YQ. From thermodynamics to kinetics: enhanced sampling of rare events. Accounts of Chemical Research. 48: 947-55. PMID 25781363 DOI: 10.1021/Ar500267N  0.667
2013 Zhang W, Rui L, Zhang J, Yu X, Yuan F, Yan L, Zhang Z, Wan Z, Shao Q, Qi C, Li Z. Production of chimeras between the Chinese soft-shelled turtle and Peking duck through transfer of early blastoderm cells. The Journal of Experimental Biology. 216: 1786-92. PMID 23348946 DOI: 10.1242/Jeb.072843  0.38
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