Jian Zhang

According to our database, Jian Zhang authored at least 32 papers between 2010 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Improving AlphaFlow for Efficient Protein Ensembles Generation.

Shaoning Li, Mingyu Li, Yusong Wang, Xinheng He, Nanning Zheng, Jian Zhang, Pheng-Ann Heng

CoRR, 2024

F³low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching.

Shaoning Li, Yusong Wang, Mingyu Li, Jian Zhang, Bin Shao, Nanning Zheng, Jian Tang

CoRR, 2024

2023

AlloReverse: multiscale understanding among hierarchical allosteric regulations.

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

Nucleic Acids Res., July, 2023

DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations.

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

Nucleic Acids Res., July, 2023

Research and Evaluation of the Allosteric Protein-Specific Force Field Based on a Pre-Training Deep Learning Model.

Xiaoyue Ji, Xiaochen Cui, Zhengxin Li, Taeyoung Choi, Ying Wang, Wen Xiao, Yunshuo Zhao, Jinyin Zha, Jian Zhang, Hai-Feng Chen, Zhengtian Yu

J. Chem. Inf. Model., April, 2023

PTMint database of experimentally verified PTM regulation on protein-protein interaction.

Xiaokun Hong, Ningshan Li, Jiyang Lv, Yan Zhang, Jing Li, Jian Zhang, Hai-Feng Chen

Bioinform., January, 2023

2022

Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation.

Hao Zhang, Duan Ni, Jigang Fan, Minyu Li, Jian Zhang, Chen Hua, Ruth Nussinov, Shaoyong Lu

J. Chem. Inf. Model., 2022

2021

IDDB: a comprehensive resource featuring genes, variants and characteristics associated with infertility.

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

Nucleic Acids Res., 2021

Recent Force Field Strategies for Intrinsically Disordered Proteins.

Junxi Mu, Hao Liu, Jian Zhang, Ray Luo, Hai-Feng Chen

J. Chem. Inf. Model., 2021

2020

Unraveling allosteric landscapes of allosterome with ASD.

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

Nucleic Acids Res., 2020

2019

AlloDriver: a method for the identification and analysis of cancer driver targets.

Kun Song, Qian Li, Wei Gao, Shaoyong Lu, Qiancheng Shen, Xinyi Liu, Yongyan Wu, Binquan Wang, Houwen Lin, Guoqiang Chen, Jian Zhang

Nucleic Acids Res., 2019

CoDockPP: A Multistage Approach for Global and Site-Specific Protein-Protein Docking.

Ren Kong, Feng Wang, Jian Zhang, Fengfei Wang, Shan Chang

J. Chem. Inf. Model., 2019

Are the Apo Proteins Suitable for the Rational Discovery of Allosteric Drugs?

Xiaoli An, Shaoyong Lu, Kun Song, Qiancheng Shen, Meilan Huang, Xiaojun Yao, Huanxiang Liu, Jian Zhang

J. Chem. Inf. Model., 2019

2018

AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses.

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

Nucleic Acids Res., 2018

2017

Improved Method for the Identification and Validation of Allosteric Sites.

Kun Song, Xinyi Liu, Wenkang Huang, Shaoyong Lu, Qiancheng Shen, Lu Zhang, Jian Zhang

J. Chem. Inf. Model., September, 2017

2016

ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks.

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

Nucleic Acids Res., 2016

Alloscore: a method for predicting allosteric ligand-protein interactions.

Shuai Li, Qiancheng Shen, Minyi Su, Xinyi Liu, Shaoyong Lu, Zhongjie Chen, Renxiao Wang, Jian Zhang

Bioinform., 2016

ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions.

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

Database J. Biol. Databases Curation, 2016

2015

ASBench: benchmarking sets for allosteric discovery.

Wenkang Huang, Guanqiao Wang, Qiancheng Shen, Xinyi Liu, Shaoyong Lu, Lv Geng, Zhimin Huang, Jian Zhang

Bioinform., 2015

2014

The Structural Basis of ATP as an Allosteric Modulator.

Shaoyong Lu, Wenkang Huang, Qi Wang, Qiancheng Shen, Shuai Li, Ruth Nussinov, Jian Zhang

PLoS Comput. Biol., 2014

ASD v2.0: updated content and novel features focusing on allosteric regulation.

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

Nucleic Acids Res., 2014

MORT: a powerful foundational library for computational biology and CADD.

Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang, Jian Zhang, Tingjun Hou

J. Cheminformatics, 2014

2013

Exploring the Desumoylation Process of SENP1: A Study Combined MD Simulations with QM/MM Calculations on SENP1-SUMO1-RanGAP1.

Ting Shi, Yuhui Han, Weihua Li, Yanlong Zhao, Yaqin Liu, Zhimin Huang, Shaoyong Lu, Jian Zhang

J. Chem. Inf. Model., 2013

How to Improve Docking Accuracy of AutoDock4.2: A Case Study Using Different Electrostatic Potentials.

Xuben Hou, Jintong Du, Jian Zhang, Lupei Du, Hao Fang, Minyong Li

J. Chem. Inf. Model., 2013

Allosite: a method for predicting allosteric sites.

Wenkang Huang, Shaoyong Lu, Zhimin Huang, Xinyi Liu, Linkai Mou, Yu Luo, Yanlong Zhao, Yaqin Liu, Zhongjie Chen, Tingjun Hou, Jian Zhang

Bioinform., 2013

2012

Insights into the Role of Magnesium Triad in <i>myo</i>-Inositol Monophosphatase: Metal Mechanism, Substrate Binding, and Lithium Therapy.

Shaoyong Lu, Wenkang Huang, Xiaobai Li, Zhimin Huang, Xinyi Liu, Yingyi Chen, Ting Shi, Jian Zhang

J. Chem. Inf. Model., 2012

Unbinding Pathways of GW4064 from Human Farnesoid X Receptor As Revealed by Molecular Dynamics Simulations.

Weihua Li, Jing Fu, Feixiong Cheng, Mingyue Zheng, Jian Zhang, Guixia Liu, Yun Tang

J. Chem. Inf. Model., 2012

2011

ASD: a comprehensive database of allosteric proteins and modulators.

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

Nucleic Acids Res., 2011

Computational Screening for Active Compounds Targeting Protein Sequences: Methodology and Experimental Validation.

Fei Wang, DongXiang Liu, Heyao Wang, Cheng Luo, Mingyue Zheng, Hong Liu, Weiliang Zhu, Xiaomin Luo, Jian Zhang, Hualiang Jiang

J. Chem. Inf. Model., 2011

ODORactor: a web server for deciphering olfactory coding.

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

Bioinform., 2011

2010

Computational Modeling Toward Understanding Agonist Binding on Dopamine 3.

Yaxue Zhao, Xuefeng Lu, Chao-Yie Yang, Zhimin Huang, Wei Fu, Tingjun Hou, Jian Zhang

J. Chem. Inf. Model., 2010

Structure-Based Design of Peptides against G3BP with Cytotoxicity on Tumor Cells.

Wei Cui, Zhuo Wei, Quan Chen, Yuanhua Cheng, Lingling Geng, Jian Zhang, Jianhua Chen, Tingjun Hou, Mingjuan Ji

J. Chem. Inf. Model., 2010