Works by Zhang, John Z. H.

Results: 61

HobPre: accurate prediction of human oral bioavailability for small molecules.

Published in:

Journal of Cheminformatics, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13321-021-00580-6

By:

Wei, Min;
Zhang, Xudong;
Pan, Xiaolin;
Wang, Bo;
Ji, Changge;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Crius: A novel fragment‐based algorithm of de novo substrate prediction for enzymes.

Published in:

Protein Science: A Publication of the Protein Society, 2018, v. 27, n. 8, p. 1526, doi. 10.1002/pro.3437

By:

Yao, Zhiqiang;
Jiang, Shuiqin;
Zhang, Lujia;
Gao, Bei;
He, Xiao;
Zhang, John Z. H.;
Wei, Dongzhi

Publication type:

Article

DeepBindGCN: Integrating Molecular Vector Representation with Graph Convolutional Neural Networks for Protein–Ligand Interaction Prediction.

Published in:

Molecules, 2023, v. 28, n. 12, p. 4691, doi. 10.3390/molecules28124691

By:

Zhang, Haiping;
Saravanan, Konda Mani;
Zhang, John Z. H.

Publication type:

Article

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host–Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation.

Published in:

Molecules, 2023, v. 28, n. 6, p. 2767, doi. 10.3390/molecules28062767

By:

Liu, Xiao;
Zheng, Lei;
Qin, Chu;
Cong, Yalong;
Zhang, John Z. H.;
Sun, Zhaoxi

Publication type:

Article

Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion.

Published in:

Molecules, 2021, v. 26, n. 11, p. 3120, doi. 10.3390/molecules26113120

By:

Cao, Liqun;
Zeng, Jinzhe;
Xu, Mingyuan;
Chin, Chih-Hao;
Zhu, Tong;
Zhang, John Z. H.

Publication type:

Article

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant.

Published in:

Journal of Computer-Aided Molecular Design, 2022, v. 36, n. 12, p. 879, doi. 10.1007/s10822-022-00487-w

By:

Liu, Xiao;
Zheng, Lei;
Cong, Yalong;
Gong, Zhihao;
Yin, Zhixiang;
Zhang, John Z. H.;
Liu, Zhirong;
Sun, Zhaoxi

Publication type:

Article

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedure.

Published in:

Journal of Computer-Aided Molecular Design, 2022, v. 36, n. 10, p. 735, doi. 10.1007/s10822-022-00475-0

By:

Liu, Xiao;
Zheng, Lei;
Qin, Chu;
Zhang, John Z. H.;
Sun, Zhaoxi

Publication type:

Article

Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation.

Published in:

Applied Microbiology & Biotechnology, 2024, v. 108, n. 1, p. 1, doi. 10.1007/s00253-023-12867-9

By:

Zhang, Xingyi;
Feng, Yinghui;
Hua, Yuanzhe;
Zhang, Chuanxi;
Fang, Bohuan;
Long, Xiang;
Pan, Yue;
Gao, Bei;
Zhang, John Z. H.;
Li, Lijun;
Ni, Hui;
Zhang, Lujia

Publication type:

Article

Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation.

Published in:

Applied Microbiology & Biotechnology, 2024, v. 108, n. 1, p. 1, doi. 10.1007/s00253-023-12867-9

By:

Zhang, Xingyi;
Feng, Yinghui;
Hua, Yuanzhe;
Zhang, Chuanxi;
Fang, Bohuan;
Long, Xiang;
Pan, Yue;
Gao, Bei;
Zhang, John Z. H.;
Li, Lijun;
Ni, Hui;
Zhang, Lujia

Publication type:

Article

Revealing the Sequence Characteristics and Molecular Mechanisms of ACE Inhibitory Peptides by Comprehensive Characterization of 160,000 Tetrapeptides.

Published in:

Foods, 2023, v. 12, n. 8, p. 1573, doi. 10.3390/foods12081573

By:

Ma, Mingzhe;
Feng, Yinghui;
Miao, Yulu;
Shen, Qiang;
Tang, Shuting;
Dong, Juan;
Zhang, John Z. H.;
Zhang, Lujia

Publication type:

Article

Discovery of novel inhibitors of SARS-CoV-2 main protease.

Published in:

Journal of Biomolecular Structure & Dynamics, 2022, v. 40, n. 23, p. 12526, doi. 10.1080/07391102.2021.1972041

By:

Zheng, Lei;
Chen, Yanmei;
Bao, Jingxiao;
He, Liping;
Dong, Suzhen;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor.

Published in:

Journal of Biomolecular Structure & Dynamics, 2021, v. 39, n. 5, p. 1588, doi. 10.1080/07391102.2020.1734488

By:

Cong, Yalong;
Duan, Lili;
Huang, Kaifang;
Bao, Jinxiao;
Zhang, John Z. H.

Publication type:

Article

Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarization.

Published in:

Journal of Biomolecular Structure & Dynamics, 2021, v. 39, n. 2, p. 743, doi. 10.1080/07391102.2020.1713892

By:

Tian, Shuaizhen;
Ji, Changge;
Zhang, John Z. H.

Publication type:

Article

Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies.

Published in:

Journal of Biomolecular Structure & Dynamics, 2020, v. 38, n. 7, p. 2141, doi. 10.1080/07391102.2019.1624616

By:

chen, Jianzhong;
Yin, Baohua;
Pang, Laixue;
Wang, Wei;
Zhang, John Z. H.;
Zhu, Tong

Publication type:

Article

Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations.

Published in:

Journal of Biomolecular Structure & Dynamics, 2020, v. 38, n. 4, p. 985, doi. 10.1080/07391102.2019.1591304

By:

Chen, Jianzhong;
Pang, Laixue;
Wang, Wei;
Wang, Lifei;
Zhang, John Z. H.;
Zhu, Tong

Publication type:

Article

An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O2 in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy.

Published in:

Angewandte Chemie International Edition, 2017, v. 56, n. 35, p. 10471, doi. 10.1002/anie.201705615

By:

Liu, Li;
Zhao, Fan;
Liu, Wei;
Zhu, Tong;
Zhang, John Z. H.;
Chen, Chen;
Dai, Zhihui;
Peng, Huisheng;
Huang, Jun-Long;
Hu, Qin;
Bu, Wenbo;
Tian, Yang

Publication type:

Article

Discovery of novel inhibitors of CDK2 using docking and physics‐based binding free energy calculation.

Published in:

Chemical Biology & Drug Design, 2022, v. 99, n. 5, p. 662, doi. 10.1111/cbdd.14027

By:

Zheng, Lei;
Yang, Yunpeng;
Bao, Jingxiao;
He, Liping;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Analysis of the binding modes of the first‐ and second‐generation antiandrogens with respect to F876L mutation.

Published in:

Chemical Biology & Drug Design, 2021, v. 98, n. 1, p. 60, doi. 10.1111/cbdd.13848

By:

Shao, Guangfeng;
Bao, Jingxiao;
Pan, Xiaolin;
He, Xiao;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Identification of three new compounds that directly target human serine hydroxymethyltransferase 2.

Published in:

Chemical Biology & Drug Design, 2021, v. 97, n. 2, p. 221, doi. 10.1111/cbdd.13774

By:

Han, Yanfang;
He, Liping;
Qi, Yifei;
Zhao, Yue;
Pan, Yue;
Fang, Bohuan;
Li, Sha;
Zhang, John Z. H.;
Zhang, Lujia

Publication type:

Article

Binding Modes of Small‐Molecule Inhibitors to the EED Pocket of PRC2.

Published in:

ChemPhysChem, 2020, v. 21, n. 3, p. 263, doi. 10.1002/cphc.201900903

By:

Huang, Dading;
Tian, Shuaizhen;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Cover Feature: Rational Design of a Highly Specific Prolyl Endopeptidase To Activate the Antihypertensive Effect of Peptides (ChemBioChem 8/2023).

Published in:

ChemBioChem, 2023, v. 24, n. 8, p. 1, doi. 10.1002/cbic.202300194

By:

Ma, Mingzhe;
Cong, Yalong;
Zhang, John Z. H.;
Zhang, Lujia

Publication type:

Article

Rational Design of a Highly Specific Prolyl Endopeptidase To Activate the Antihypertensive Effect of Peptides.

Published in:

ChemBioChem, 2023, v. 24, n. 8, p. 1, doi. 10.1002/cbic.202200691

By:

Ma, Mingzhe;
Cong, Yalong;
Zhang, John Z. H.;
Zhang, Lujia

Publication type:

Article

Functional Loop Dynamics of the Streptavidin-Biotin Complex.

Published in:

Scientific Reports, 2015, p. 7906, doi. 10.1038/srep07906

By:

Song, Jianing;
Li, Yongle;
Ji, Changge;
Zhang, John Z. H.

Publication type:

Article

Unveiling the gating mechanism of ECF Transporter RibU.

Published in:

Scientific Reports, 2013, p. 1, doi. 10.1038/srep03566

By:

Jianing Song;
Changge Ji;
John Z. H. Zhang

Publication type:

Article

Interaction entropy for computational alanine scanning in protein–protein binding.

Published in:

WIREs: Computational Molecular Science, 2018, v. 8, n. 2, p. 1, doi. 10.1002/wcms.1342

By:

Qiu, Linqiong;
Yan, Yuna;
Sun, Zhaoxi;
Song, Jianing;
Zhang, John Z. H.

Publication type:

Article

An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O2 in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy.

Published in:

Angewandte Chemie, 2017, v. 129, n. 35, p. 10607, doi. 10.1002/ange.201705615

By:

Liu, Li;
Zhao, Fan;
Liu, Wei;
Zhu, Tong;
Zhang, John Z. H.;
Chen, Chen;
Dai, Zhihui;
Peng, Huisheng;
Huang, Jun‐Long;
Hu, Qin;
Bu, Wenbo;
Tian, Yang

Publication type:

Article

SeBPPI: A Sequence-Based Protein–Protein Binding Predictor.

Published in:

Journal of Computational Biophysics & Chemistry, 2022, v. 21, n. 6, p. 729, doi. 10.1142/S2737416522500314

By:

Wang, Bo;
Mao, Jun;
Wei, Min;
Qi, Yifei;
Zhang, John Z. H.

Publication type:

Article

Total and partial decay widths in vibrational predissociation of the HeI2 van der Waals complex for lower initial vibrational excitations.

Published in:

International Journal of Quantum Chemistry, 1997, v. 62, n. 1, p. 89, doi. 10.1002/(SICI)1097-461X(1997)62:1<89::AID-QUA9>3.0.CO;2-#

By:

Guan, Daren;
Zhao, Xian;
Deng, Conghao;
Zhang, John Z. H.

Publication type:

Article

BAR‐based optimum adaptive steered MD for configurational sampling.

Published in:

Journal of Computational Chemistry, 2019, v. 40, n. 12, p. 1270, doi. 10.1002/jcc.25784

By:

Wang, Xiaohui;
Tu, Xingzhao;
Deng, Boming;
Zhang, John Z. H.;
Sun, Zhaoxi

Publication type:

Article

Calculation of hot spots for protein–protein interaction in p53/PMI‐MDM2/MDMX complexes.

Published in:

Journal of Computational Chemistry, 2019, v. 40, n. 9, p. 1045, doi. 10.1002/jcc.25592

By:

Huang, Dading;
Qi, Yifei;
Song, Jianing;
Zhang, John Z. H.

Publication type:

Article

A new algorithm for construction of coarse-grained sites of large biomolecules.

Published in:

Journal of Computational Chemistry, 2016, v. 37, n. 9, p. 795, doi. 10.1002/jcc.24265

By:

Li, Min;
Zhang, John Z. H.;
Xia, Fei

Publication type:

Article

Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis.

Published in:

Journal of Computational Chemistry, 2014, v. 35, n. 9, p. 737, doi. 10.1002/jcc.23547

By:

Jia, Xiangyu;
Zeng, Juan;
Zhang, John Z. H.;
Mei, Ye

Publication type:

Article

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect.

Published in:

Journal of Computational Chemistry, 2013, v. 34, n. 31, p. 2677, doi. 10.1002/jcc.23421

By:

Zeng, Juan;
Jia, Xiangyu;
Zhang, John Z. H.;
Mei, Ye

Publication type:

Article

Identification and Validation of New DNA-PKcs Inhibitors through High-Throughput Virtual Screening and Experimental Verification.

Published in:

International Journal of Molecular Sciences, 2024, v. 25, n. 14, p. 7982, doi. 10.3390/ijms25147982

By:

Dai, Liujiang;
Yu, Pengfei;
Fan, Hongjie;
Xia, Wei;
Zhao, Yaopeng;
Zhang, Pengfei;
Zhang, John Z. H.;
Zhang, Haiping;
Chen, Yang

Publication type:

Article

Selectivity of Neutral/Weakly Basic P1 Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study.

Published in:

Chemistry - A European Journal, 2008, v. 14, n. 28, p. 8704, doi. 10.1002/chem.200800277

By:

Wu, Emilia L.;
Han, KeLi;
Zhang, John Z. H.

Publication type:

Article

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 13, p. 6618, doi. 10.1093/nar/gkz499

By:

Chen, Jianzhong;
Wang, Xingyu;
Pang, Laixue;
Zhang, John Z H;
Zhu, Tong

Publication type:

Article

Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations.

Published in:

Scientific Reports, 2017, p. 42223, doi. 10.1038/srep42223

By:

Duan, Li L.;
Zhu, T.;
Li, Yu C.;
Zhang, Qing G.;
Zhang, John Z. H.

Publication type:

Article

The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations.

Published in:

Scientific Reports, 2016, p. 27190, doi. 10.1038/srep27190

By:

Liu, Fengjiao;
Zhang, John Z. H.;
Mei, Ye

Publication type:

Article

Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-19497-z

By:

Zeng, Jinzhe;
Cao, Liqun;
Xu, Mingyuan;
Zhu, Tong;
Zhang, John Z. H.

Publication type:

Article

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

Published in:

Molecular Physics, 2018, v. 116, n. 19/20, p. 2613, doi. 10.1080/00268976.2018.1467052

By:

Qiu, Linqiong;
Shen, Cong;
Song, Jianing;
Zhang, Yingkai;
Zhang, John Z. H.

Publication type:

Article

Residue-specific free energy analysis in ligand bindings to JAK2.

Published in:

Molecular Physics, 2018, v. 116, n. 19/20, p. 2633, doi. 10.1080/00268976.2018.1442596

By:

Zhou, Yifan;
Liu, Xiao;
Zhang, Youzhi;
Peng, Long;
Zhang, John Z. H.

Publication type:

Article

Effect of Self-Assembly of Fullerene Nano-Particles on Lipid Membrane.

Published in:

PLoS ONE, 2013, v. 8, n. 10, p. 1, doi. 10.1371/journal.pone.0077436

By:

Zhang, Saiqun;
Mu, Yuguang;
Zhang, John Z. H.;
Xu, Weixin

Publication type:

Article

Full quantum mechanical study of binding of HIV-1 protease drugs.

Published in:

International Journal of Quantum Chemistry, 2005, v. 103, n. 3, p. 246, doi. 10.1002/qua.20488

By:

Zhang, Da W.;
Zhang, John Z. H.

Publication type:

Article

Effect of Interprotein Polarization on Protein-Protein Binding Energy.

Published in:

Journal of Computational Chemistry, 2012, v. 33, n. 16, p. 1416, doi. 10.1002/jcc.22969

By:

Ji, Chang G.;
Zhang, John Z. H.

Publication type:

Article

Electrostatic polarization is critical for the strong binding in streptavidin-biotin system.

Published in:

Journal of Computational Chemistry, 2012, v. 33, n. 15, p. 1374, doi. 10.1002/jcc.22970

By:

Mei, Ye;
Li, Yong L.;
Zeng, Juan;
Zhang, John Z. H.

Publication type:

Article

Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions.

Published in:

Journal of Computational Chemistry, 2009, v. 30, n. 2, p. 305, doi. 10.1002/jcc.21032

By:

Li-Ping Ju;
Ke-Li Han;
John Z. H. Zhang

Publication type:

Article

Efficient bond function basis set for π-π interaction energies.

Published in:

Journal of Computational Chemistry, 2008, v. 29, n. 2, p. 275, doi. 10.1002/jcc.20788

By:

Yun Ding;
Ye Mei;
Zhang, John Z. H.;
Fu-Ming Tao

Publication type:

Article

Fully quantum mechanical energy optimization for protein-ligand structure.

Published in:

Journal of Computational Chemistry, 2004, v. 25, n. 12, p. 1431, doi. 10.1002/jcc.20069

By:

Xiang, Yun;
Zhang, Da W.;
Zhang, John Z. H.

Publication type:

Article

Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like protease.

Published in:

Cellular & Molecular Life Sciences, 2023, v. 80, n. 11, p. 1, doi. 10.1007/s00018-023-04985-4

By:

Duan, Lili;
Tang, Bolin;
Luo, Song;
Xiong, Danyang;
Wang, Qihang;
Xu, Xiaole;
Zhang, John Z. H.

Publication type:

Article

Insights on Na+ binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM.

Published in:

Proteins, 2014, v. 82, n. 2, p. 240, doi. 10.1002/prot.24368

By:

Song, Jianing;
Ji, Changge;
Zhang, John Z. H.

Publication type:

Article