TarFisDock: a web server for identifying drug targets with docking approach. - Honglin Li 003; Zhenting Gao; Ling Kang; Hailei Zhang; Kun Yang; Kunqian Yu; Xiaomin Luo; Weiliang Zhu; Kaixian Chen; Jianhua Shen; Xicheng Wang; Hualiang Jiang (Nucleic Acids Res., 2006)

PDTD: a web-accessible protein database for drug target identification. - Zhenting Gao; Honglin Li 003; Hailei Zhang; Xiaofeng Liu 005; Ling Kang; Xiaomin Luo; Weiliang Zhu; Kaixian Chen; Xicheng Wang; Hualiang Jiang (BMC Bioinform., 2008)

An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA. - Xiaoyu Zhao; Xiaofeng Liu 005; Yuanyuan Wang; Zhi Chen; Ling Kang; Hailei Zhang; Xiaomin Luo; Weiliang Zhu; Kaixian Chen; Honglin Li 003; Xicheng Wang; Hualiang Jiang (J. Chem. Inf. Model., 2008)

Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor. - Xinli Liu; Yechun Xu; Honglin Li 003; Xicheng Wang; Hualiang Jiang; Francisco J. Barrantes (PLoS Comput. Biol., 2008)

An effective docking strategy for virtual screening based on multi-objective optimization algorithm. - Honglin Li 003; Hailei Zhang; Mingyue Zheng; Jie Luo; Ling Kang; Xiaofeng Liu 005; Xicheng Wang; Hualiang Jiang (BMC Bioinform., 2009)

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation. - Xiaofeng Liu 005; Fang Bai; Sisheng Ouyang; Xicheng Wang; Honglin Li 003; Hualiang Jiang (BMC Bioinform., 2009)

An improved adaptive genetic algorithm for protein-ligand docking. - Ling Kang; Honglin Li 003; Hualiang Jiang; Xicheng Wang (J. Comput. Aided Mol. Des., 2009)

Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function. - Junfeng Gu; Honglin Li 003; Hualiang Jiang; Xicheng Wang (J. Comput. Biol., 2009)

Bioactive Conformational Generation of Small Molecules: A Comparative Analysis between Force-Field and Multiple Empirical Criteria Based Methods. - Fang Bai; Xiaofeng Liu 005; Jiabo Li; Haoyun Zhang; Hualiang Jiang; Xicheng Wang; Honglin Li 003 (BMC Bioinform., 2010)

PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. - Xiaofeng Liu 005; Sisheng Ouyang; Biao Yu; Yabo Liu; Kai Huang; Jiayu Gong; Siyuan Zheng; Zhihua Li; Honglin Li 003; Hualiang Jiang (Nucleic Acids Res., 2010)

Identification of Inhibitors against p90 Ribosomal S6 Kinase 2 (RSK2) through Structure-Based Virtual Screening with the Inhibitor-Constrained Refined Homology Model. - Shiliang Li; Yi Zhou; Weiqiang Lu; Ye Zhong; Wenlong Song; Kangdong Liu; Jin Huang; Zhenjiang Zhao; Yufang Xu; Xiaofeng Liu 005; Honglin Li 003 (J. Chem. Inf. Model., 2011)

SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening. - Xiaofeng Liu 005; Hualiang Jiang; Honglin Li 003 (J. Chem. Inf. Model., 2011)

ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method. - Jiayu Gong; Chaoqian Cai; Xiaofeng Liu 005; Xin Ku; Hualiang Jiang; Daqi Gao; Honglin Li 003 (Bioinform., 2013)

PTID: an integrated web resource and computational tool for agrochemical discovery. - Jiayu Gong; Xiaofeng Liu 005; Xianwen Cao; Yanyan Diao; Daqi Gao; Honglin Li 003; Xuhong Qian (Bioinform., 2013)

An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis. - Chuanxin Zou; Jiayu Gong; Honglin Li 003 (BMC Bioinform., 2013)

SimG: An Alignment Based Method for Evaluating the Similarity of Small Molecules and Binding Sites. - Chaoqian Cai; Jiayu Gong; Xiaofeng Liu 005; Daqi Gao; Honglin Li 003 (J. Chem. Inf. Model., 2013)

iDrug: a web-accessible and interactive drug discovery and design platform. - Xia Wang; Haipeng Chen; Feng Yang; Jiayu Gong; Shiliang Li; Jianfeng Pei; Xiaofeng Liu 005; Hualiang Jiang; Luhua Lai; Honglin Li 003 (J. Cheminformatics, 2014)

An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy. - Fang Bai; Sha Liao; Junfeng Gu; Hualiang Jiang; Xicheng Wang; Honglin Li 003 (J. Chem. Inf. Model., 2015)

Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors. - Meijian Sun; Xia Wang; Chuanxin Zou; Zenghui He; Wei Liu; Honglin Li 003 (BMC Bioinform., 2016)

Enhancing the Enrichment of Pharmacophore-Based Target Prediction for the Polypharmacological Profiles of Drugs. - Xia Wang; Chenxu Pan; Jiayu Gong; Xiaofeng Liu 005; Honglin Li 003 (J. Chem. Inf. Model., 2016)

PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database. - Xia Wang; Yihang Shen; Shiwei Wang; Shiliang Li; Weilin Zhang; Xiaofeng Liu 005; Luhua Lai; Jianfeng Pei; Honglin Li 003 (Nucleic Acids Res., 2017)

Statistical Analysis, Investigation, and Prediction of the Water Positions in the Binding Sites of Proteins. - Wei Xiao; Zenghui He; Meijian Sun; Shiliang Li; Honglin Li 003 (J. Chem. Inf. Model., 2017)

eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity. - Gaoqi He; Yiping Song; Wenhao Wei; Xia Wang; Xingjian Lu; Honglin Li 003 (J. Comput. Chem., 2019)

Pharmacodynamics simulation of HOEC by a computational model of arachidonic acid metabolic network. - Wen Yang; Xia Wang; Kenan Li; Yuanru Liu; Ying Liu; Rui Wang; Honglin Li 003 (Quant. Biol., 2019)

Computational Insight into the Allosteric Activation Mechanism of Farnesoid X Receptor. - Yue Chen; Junhao Li; Zengrui Wu; Guixia Liu; Honglin Li 003; Yun Tang 001; Weihua Li 005 (J. Chem. Inf. Model., 2020)

NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data. - Qingxia Yang; Yunxia Wang; Ying Zhang 061; Fengcheng Li; Weiqi Xia; Ying Zhou; Yunqing Qiu; Honglin Li 003; Feng Zhu 004 (Nucleic Acids Res., 2020)

Cover Image. - Yuxia Mao; Shiliang Li; Bojie Gong; Luhua Lai; Gaoqi He; Honglin Li 003 (J. Comput. Chem., 2021)

ePharmer: An integrated and graphical software for pharmacophore-based virtual screening. - Yuxia Mao; Shiliang Li; Bojie Gong; Luhua Lai; Gaoqi He; Honglin Li 003 (J. Comput. Chem., 2021)

e-TSN: an interactive visual exploration platform for target-disease knowledge mapping from literature. - Ziyan Feng; Zihao Shen; Honglin Li 003; Shiliang Li (Briefings Bioinform., 2022)

Multi-modal chemical information reconstruction from images and texts for exploring the near-drug space. - Jie Wang 146; Zihao Shen; Yichen Liao; Zhen Yuan; Shiliang Li; Gaoqi He; Man Lan; Xuhong Qian; Kai Zhang 001; Honglin Li 003 (Briefings Bioinform., 2022)

Comprehensive assessment of deep generative architectures for de novo drug design. - Mingyang Wang 004; Huiyong Sun; Jike Wang; Jinping Pang; Xin Chai; Lei Xu 035; Honglin Li 003; Dongsheng Cao 001; Tingjun Hou (Briefings Bioinform., 2022)

ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA. - Hanyu Zhang; Yunxia Wang; Ziqi Pan; Xiuna Sun; Minjie Mou; Bing Zhang; Zhaorong Li; Honglin Li 003; Feng Zhu 004 (Briefings Bioinform., 2022)

PFmulDL: a novel strategy enabling multi-class and multi-label protein function annotation by integrating diverse deep learning methods. - Weiqi Xia; Lingyan Zheng; Jiebin Fang; Fengcheng Li; Ying Zhou; Zhenyu Zeng; Bing Zhang; Zhaorong Li; Honglin Li 003; Feng Zhu 004 (Comput. Biol. Medicine, 2022)

ReMODE: a deep learning-based web server for target-specific drug design. - Mingyang Wang 004; Jike Wang; Gaoqi Weng; Yu Kang 002; Peichen Pan; Dan Li 013; Yafeng Deng; Honglin Li 003; Chang-Yu Hsieh; Tingjun Hou (J. Cheminformatics, 2022)

SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer. - Zhanpeng Xu; Jianhua Li; Zhaopeng Yang; Shiliang Li; Honglin Li 003 (J. Cheminformatics, 2022)

Molecular Docking for Ligand-Receptor Binding Process Based on Heterogeneous Computing. - Jianhua Li; Guanlong Liu; Zhiyuan Zhen; Zihao Shen; Shiliang Li; Honglin Li 003 (Sci. Program., 2022)

VRPharmer: bringing virtual reality into pharmacophore-based virtual screening with interactive exploration and realistic visualization. - Shun Liu; Jianchao Zhou; Ziyan Feng; Jiawen Zhang; Shuang Li; Zilong Jin; Chenfei Zhang; Shiliang Li; Gaoqi He; Honglin Li 003 (Bioinform., 2022)

MacFrag: segmenting large-scale molecules to obtain diverse fragments with high qualities. - Yanyan Diao; Feng Hu; Zihao Shen; Honglin Li 003 (Bioinform., 2023)

RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction. - Yunxia Wang; Zhen Chen; Ziqi Pan; Shijie Huang; Jin Liu; Weiqi Xia; Hongning Zhang; Mingyue Zheng; Honglin Li 003; Tingjun Hou; Feng Zhu 004 (Nucleic Acids Res., 2023)

Knowledge Graph Information Bottleneck for Drug-Drug Interaction Prediction. - Shun Liu; Gaoqi He; Kai Zhang 001; Honglin Li 003 (IJCNN, 2024)

Prototype-based contrastive substructure identification for molecular property prediction. - Gaoqi He; Shun Liu; Zhuoran Liu; Changbo Wang; Kai Zhang 001; Honglin Li 003 (Briefings Bioinform., 2024)

Enhancing Chemical Reaction Monitoring with a Deep Learning Model for NMR Spectra Image Matching to Target Compounds. - Zijing Tian; Yan Dai 013; Feng Hu; Zihao Shen; Hongling Xu; Hongwen Zhang 008; Jinhang Xu; Yuting Hu; Yanyan Diao; Honglin Li 003 (J. Chem. Inf. Model., 2024)

Sliding-attention transformer neural architecture for predicting T cell receptor-antigen-human leucocyte antigen binding. - Ziyan Feng; Jingyang Chen; Youlong Hai; Xuelian Pang; Kun Zheng; Chenglong Xie; Xiujuan Zhang; Shengqing Li; Chengjuan Zhang; Kangdong Liu; Lili Zhu; Xiaoyong Hu; et al. (Nat. Mac. Intell., 2024)

MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. - Lingyan Zheng; Shuiyang Shi; Xiuna Sun; Mingkun Lu; Yang Liao; Sisi Zhu; Hongning Zhang; Ziqi Pan; Pan Fang; Zhenyu Zeng; Honglin Li 003; Zhaorong Li; et al. (Briefings Bioinform., 2024)

A Transformative Topological Representation for Link Modeling, Prediction and Cross-Domain Network Analysis. - Kai Zhang 001; Junchen Shen; Gaoqi He; Yu Sun; Haibin Ling; Hongyuan Zha; Honglin Li 003; Jie Zhang 012 (IEEE Trans. Pattern Anal. Mach. Intell., 2024)

RPSubAlign: a novel sequence-based molecular representation method for retrosynthesis prediction with improved validity and robustness. - Yuting Hu; Feng Hu; Hongwen Zhang 008; Hongling Xu; Jixiang Gao; Wenshuai Deng; Zijing Tian; Qiaoyu Hu; Honglin Li 003; Yanyan Diao (Briefings Bioinform., 2025)

Decoding Drug Response With Structurized Gridding Map-Based Cell Representation. - Jiayi Yin; Hanyu Zhang; Xiuna Sun; Nanxin You; Minjie Mou; Mingkun Lu; Ziqi Pan; Fengcheng Li; Honglin Li 003; Su Zeng; Feng Zhu 004 (IEEE J. Biomed. Health Informatics, 2025)