Jian Zhang

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 16

Top Topics

Computational Biology

Experimentally Verified

Top Venues

Nucleic Acids Res.

J. Chem. Inf. Model.

Publications

Shaoning Li, Mingyu Li, Yusong Wang, Xinheng He, Nanning Zheng, Jian Zhang, Pheng-Ann Heng
Improving AlphaFlow for Efficient Protein Ensembles Generation. CoRR (2024)
Jinyin Zha, Qian Li, Xinyi Liu, Weidong Lin, Tingting Wang, Jiacheng Wei, Ziliang Zhang, Xun Lu, Jing Wu, Duan Ni, Kun Song, Liang Zhang, Xuefeng Lu, Shaoyong Lu, Jian Zhang
AlloReverse: multiscale understanding among hierarchical allosteric regulations. Nucleic Acids Res. 51 (W1) (2023)
Xiaoyue Ji, Xiaochen Cui, Zhengxin Li, Taeyoung Choi, Ying Wang, Wen Xiao, Yunshuo Zhao, Jinyin Zha, Jian Zhang, Hai-Feng Chen, Zhengtian Yu
Research and Evaluation of the Allosteric Protein-Specific Force Field Based on a Pre-Training Deep Learning Model. J. Chem. Inf. Model. 63 (8) (2023)
Qianqian Song, Mingyu Li, Qian Li, Xun Lu, Kun Song, Ziliang Zhang, Jiale Wei, Liang Zhang, Jiacheng Wei, Youqiong Ye, Jinyin Zha, Qiufen Zhang, Qiang Gao, Jiang Long, Xinyi Liu, Xuefeng Lu, Jian Zhang
DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations. Nucleic Acids Res. 51 (W1) (2023)
Xiaokun Hong, Ningshan Li, Jiyang Lv, Yan Zhang, Jing Li, Jian Zhang, Hai-Feng Chen
PTMint database of experimentally verified PTM regulation on protein-protein interaction. Bioinform. 39 (1) (2023)
Jing Wu, Danjun Li, Xinyi Liu, Qian Li, Xinheng He, Jiale Wei, Xinyi Li, Mingyu Li, Ashfaq Ur Rehman, Yujia Xia, Chengwei Wu, Jian Zhang, Xuefeng Lu
IDDB: a comprehensive resource featuring genes, variants and characteristics associated with infertility. Nucleic Acids Res. 49 (Database-Issue) (2021)
Junxi Mu, Hao Liu, Jian Zhang, Ray Luo, Hai-Feng Chen
Recent Force Field Strategies for Intrinsically Disordered Proteins. J. Chem. Inf. Model. 61 (3) (2021)
Xinyi Liu, Shaoyong Lu, Kun Song, Qiancheng Shen, Duan Ni, Qian Li, Xinheng He, Hao Zhang, Qi Wang, Yingyi Chen, Xinyi Li, Jing Wu, Chunquan Sheng, Guoqiang Chen, Yaqin Liu, Xuefeng Lu, Jian Zhang
Unraveling allosteric landscapes of allosterome with ASD. Nucleic Acids Res. 48 (Database-Issue) (2020)
Ren Kong, Feng Wang, Jian Zhang, Fengfei Wang, Shan Chang
CoDockPP: A Multistage Approach for Global and Site-Specific Protein-Protein Docking. J. Chem. Inf. Model. 59 (8) (2019)
Xiaoli An, Shaoyong Lu, Kun Song, Qiancheng Shen, Meilan Huang, Xiaojun Yao, Huanxiang Liu, Jian Zhang
Are the Apo Proteins Suitable for the Rational Discovery of Allosteric Drugs? J. Chem. Inf. Model. 59 (1) (2019)
Kun Song, Qian Li, Wei Gao, Shaoyong Lu, Qiancheng Shen, Xinyi Liu, Yongyan Wu, Binquan Wang, Houwen Lin, Guoqiang Chen, Jian Zhang
AlloDriver: a method for the identification and analysis of cancer driver targets. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Min Huang, Kun Song, Xinyi Liu, Shaoyong Lu, Qiancheng Shen, Renxiao Wang, Jingze Gao, Yuanyuan Hong, Qian Li, Duan Ni, Jianrong Xu, Guoqiang Chen, Jian Zhang
AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Kun Song, Xinyi Liu, Wenkang Huang, Shaoyong Lu, Qiancheng Shen, Lu Zhang, Jian Zhang
Improved Method for the Identification and Validation of Allosteric Sites. J. Chem. Inf. Model. 57 (9) (2017)
Shuai Li, Qiancheng Shen, Minyi Su, Xinyi Liu, Shaoyong Lu, Zhongjie Chen, Renxiao Wang, Jian Zhang
Alloscore: a method for predicting allosteric ligand-protein interactions. Bioinform. 32 (10) (2016)
Qiancheng Shen, Guanqiao Wang, Shuai Li, Xinyi Liu, Shaoyong Lu, Zhongjie Chen, Kun Song, Junhao Yan, Lv Geng, Zhimin Huang, Wenkang Huang, Guoqiang Chen, Jian Zhang
ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks. Nucleic Acids Res. 44 (Database-Issue) (2016)
Luis N. Marenco, Rixin Wang, Robert A. McDougal, Tsviya Olender, Michal Twik, Elspeth A. Bruford, Xinyi Liu, Jian Zhang, Doron Lancet, Gordon M. Shepherd, Chiquito J. Crasto
ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. Database J. Biol. Databases Curation 2016 (2016)
Wenkang Huang, Guanqiao Wang, Qiancheng Shen, Xinyi Liu, Shaoyong Lu, Lv Geng, Zhimin Huang, Jian Zhang
ASBench: benchmarking sets for allosteric discovery. Bioinform. 31 (15) (2015)
Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang, Jian Zhang, Tingjun Hou
MORT: a powerful foundational library for computational biology and CADD. J. Cheminformatics 6 (1) (2014)
Zhimin Huang, Linkai Mou, Qiancheng Shen, Shaoyong Lu, Chuangang Li, Xinyi Liu, Guanqiao Wang, Shuai Li, Lv Geng, Yaqin Liu, Jiawei Wu, Guoqiang Chen, Jian Zhang
ASD v2.0: updated content and novel features focusing on allosteric regulation. Nucleic Acids Res. 42 (Database-Issue) (2014)
Shaoyong Lu, Wenkang Huang, Qi Wang, Qiancheng Shen, Shuai Li, Ruth Nussinov, Jian Zhang
The Structural Basis of ATP as an Allosteric Modulator. PLoS Comput. Biol. 10 (9) (2014)
Wenkang Huang, Shaoyong Lu, Zhimin Huang, Xinyi Liu, Linkai Mou, Yu Luo, Yanlong Zhao, Yaqin Liu, Zhongjie Chen, Tingjun Hou, Jian Zhang
Allosite: a method for predicting allosteric sites. Bioinform. 29 (18) (2013)
Ting Shi, Yuhui Han, Weihua Li, Yanlong Zhao, Yaqin Liu, Zhimin Huang, Shaoyong Lu, Jian Zhang
Exploring the Desumoylation Process of SENP1: A Study Combined MD Simulations with QM/MM Calculations on SENP1-SUMO1-RanGAP1. J. Chem. Inf. Model. 53 (9) (2013)
Weihua Li, Jing Fu, Feixiong Cheng, Mingyue Zheng, Jian Zhang, Guixia Liu, Yun Tang
Unbinding Pathways of GW4064 from Human Farnesoid X Receptor As Revealed by Molecular Dynamics Simulations. J. Chem. Inf. Model. 52 (11) (2012)
Shaoyong Lu, Wenkang Huang, Xiaobai Li, Zhimin Huang, Xinyi Liu, Yingyi Chen, Ting Shi, Jian Zhang
-Inositol Monophosphatase: Metal Mechanism, Substrate Binding, and Lithium Therapy. J. Chem. Inf. Model. 52 (9) (2012)
Xinyi Liu, Xubo Su, Fei Wang, Zhimin Huang, Qi Wang, Zhen Li, Ruina Zhang, Lifang Wu, Yi Pan, Yingyi Chen, Hanyi Zhuang, Guoqiang Chen, Ting Shi, Jian Zhang
ODORactor: a web server for deciphering olfactory coding. Bioinform. 27 (16) (2011)
Fei Wang, DongXiang Liu, Heyao Wang, Cheng Luo, Mingyue Zheng, Hong Liu, Weiliang Zhu, Xiaomin Luo, Jian Zhang, Hualiang Jiang
Computational Screening for Active Compounds Targeting Protein Sequences: Methodology and Experimental Validation. J. Chem. Inf. Model. 51 (11) (2011)
Zhimin Huang, Liang Zhu, Yan Cao, Geng Wu, Xinyi Liu, Yingyi Chen, Qi Wang, Ting Shi, Yaxue Zhao, Yuefei Wang, Weihua Li, Yixue Li, Haifeng Chen, Guoqiang Chen, Jian Zhang
ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Res. 39 (Database-Issue) (2011)
Yaxue Zhao, Xuefeng Lu, Chao-Yie Yang, Zhimin Huang, Wei Fu, Tingjun Hou, Jian Zhang
Computational Modeling Toward Understanding Agonist Binding on Dopamine 3. J. Chem. Inf. Model. 50 (9) (2010)
Wei Cui, Zhuo Wei, Quan Chen, Yuanhua Cheng, Lingling Geng, Jian Zhang, Jianhua Chen, Tingjun Hou, Mingjuan Ji
Structure-Based Design of Peptides against G3BP with Cytotoxicity on Tumor Cells. J. Chem. Inf. Model. 50 (3) (2010)