Honglin Li

47 papers B 1Journal 46
YearRankTypeTitle / Venue / Authors
2025 J jnl
Decoding Drug Response With Structurized Gridding Map-Based Cell Representation.
IEEE J. Biomed. Health Informatics
Jiayi Yin, Hanyu Zhang, Xiuna Sun, Nanxin You, Minjie Mou, Mingkun Lu, Ziqi Pan, Fengcheng Li, Honglin Li, Su Zeng, Feng Zhu
2025 J jnl
RPSubAlign: a novel sequence-based molecular representation method for retrosynthesis prediction with improved validity and robustness.
Briefings Bioinform.
Yuting Hu, Feng Hu, Hongwen Zhang, Hongling Xu, Jixiang Gao, Wenshuai Deng, Zijing Tian, Qiaoyu Hu, Honglin Li, Yanyan Diao
2024 J jnl
A Transformative Topological Representation for Link Modeling, Prediction and Cross-Domain Network Analysis.
IEEE Trans. Pattern Anal. Mach. Intell.
Kai Zhang, Junchen Shen, Gaoqi He, Yu Sun, Haibin Ling, Hongyuan Zha, Honglin Li, Jie Zhang
2024 J jnl
Enhancing Chemical Reaction Monitoring with a Deep Learning Model for NMR Spectra Image Matching to Target Compounds.
J. Chem. Inf. Model.
Zijing Tian, Yan Dai, Feng Hu, Zihao Shen, Hongling Xu, Hongwen Zhang, Jinhang Xu, Yuting Hu, Yanyan Diao, Honglin Li
2024 B conf
Knowledge Graph Information Bottleneck for Drug-Drug Interaction Prediction.
IJCNN
Shun Liu, Gaoqi He, Kai Zhang, Honglin Li
2024 J jnl
MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics.
Briefings Bioinform.
Lingyan Zheng, Shuiyang Shi, Xiuna Sun, Mingkun Lu, Yang Liao, Sisi Zhu, Hongning Zhang, Ziqi Pan, Pan Fang, Zhenyu Zeng, Honglin Li, Zhaorong Li, Weiwei Xue, Feng Zhu
2024 J jnl
Prototype-based contrastive substructure identification for molecular property prediction.
Briefings Bioinform.
Gaoqi He, Shun Liu, Zhuoran Liu, Changbo Wang, Kai Zhang, Honglin Li
2024 J jnl
Sliding-attention transformer neural architecture for predicting T cell receptor-antigen-human leucocyte antigen binding.
Nat. Mac. Intell.
Ziyan Feng, Jingyang Chen, Youlong Hai, Xuelian Pang, Kun Zheng, Chenglong Xie, Xiujuan Zhang, Shengqing Li, Chengjuan Zhang, Kangdong Liu, Lili Zhu, Xiaoyong Hu, Shiliang Li, Jie Zhang, Kai Zhang, Honglin Li
2023 J jnl
MacFrag: segmenting large-scale molecules to obtain diverse fragments with high qualities.
Bioinform.
Yanyan Diao, Feng Hu, Zihao Shen, Honglin Li
2023 J jnl
RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction.
Nucleic Acids Res.
Yunxia Wang, Zhen Chen, Ziqi Pan, Shijie Huang, Jin Liu, Weiqi Xia, Hongning Zhang, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu
2022 J jnl
Comprehensive assessment of deep generative architectures for de novo drug design.
Briefings Bioinform.
Mingyang Wang, Huiyong Sun, Jike Wang, Jinping Pang, Xin Chai, Lei Xu, Honglin Li, Dongsheng Cao, Tingjun Hou
2022 J jnl
Molecular Docking for Ligand-Receptor Binding Process Based on Heterogeneous Computing.
Sci. Program.
Jianhua Li, Guanlong Liu, Zhiyuan Zhen, Zihao Shen, Shiliang Li, Honglin Li
2022 J jnl
Multi-modal chemical information reconstruction from images and texts for exploring the near-drug space.
Briefings Bioinform.
Jie Wang, Zihao Shen, Yichen Liao, Zhen Yuan, Shiliang Li, Gaoqi He, Man Lan, Xuhong Qian, Kai Zhang, Honglin Li
2022 J jnl
PFmulDL: a novel strategy enabling multi-class and multi-label protein function annotation by integrating diverse deep learning methods.
Comput. Biol. Medicine
Weiqi Xia, Lingyan Zheng, Jiebin Fang, Fengcheng Li, Ying Zhou, Zhenyu Zeng, Bing Zhang, Zhaorong Li, Honglin Li, Feng Zhu
2022 J jnl
ReMODE: a deep learning-based web server for target-specific drug design.
J. Cheminformatics
Mingyang Wang, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Honglin Li, Chang-Yu Hsieh, Tingjun Hou
2022 J jnl
SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer.
J. Cheminformatics
Zhanpeng Xu, Jianhua Li, Zhaopeng Yang, Shiliang Li, Honglin Li
2022 J jnl
VRPharmer: bringing virtual reality into pharmacophore-based virtual screening with interactive exploration and realistic visualization.
Bioinform.
Shun Liu, Jianchao Zhou, Ziyan Feng, Jiawen Zhang, Shuang Li, Zilong Jin, Chenfei Zhang, Shiliang Li, Gaoqi He, Honglin Li
2022 J jnl
e-TSN: an interactive visual exploration platform for target-disease knowledge mapping from literature.
Briefings Bioinform.
Ziyan Feng, Zihao Shen, Honglin Li, Shiliang Li
2022 J jnl
ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA.
Briefings Bioinform.
Hanyu Zhang, Yunxia Wang, Ziqi Pan, Xiuna Sun, Minjie Mou, Bing Zhang, Zhaorong Li, Honglin Li, Feng Zhu
2021 J jnl
Cover Image.
J. Comput. Chem.
Yuxia Mao, Shiliang Li, Bojie Gong, Luhua Lai, Gaoqi He, Honglin Li
2021 J jnl
ePharmer: An integrated and graphical software for pharmacophore-based virtual screening.
J. Comput. Chem.
Yuxia Mao, Shiliang Li, Bojie Gong, Luhua Lai, Gaoqi He, Honglin Li
2020 J jnl
Computational Insight into the Allosteric Activation Mechanism of Farnesoid X Receptor.
J. Chem. Inf. Model.
Yue Chen, Junhao Li, Zengrui Wu, Guixia Liu, Honglin Li, Yun Tang, Weihua Li
2020 J jnl
NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data.
Nucleic Acids Res.
Qingxia Yang, Yunxia Wang, Ying Zhang, Fengcheng Li, Weiqi Xia, Ying Zhou, Yunqing Qiu, Honglin Li, Feng Zhu
2019 J jnl
Pharmacodynamics simulation of HOEC by a computational model of arachidonic acid metabolic network.
Quant. Biol.
Wen Yang, Xia Wang, Kenan Li, Yuanru Liu, Ying Liu, Rui Wang, Honglin Li
2019 J jnl
eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity.
J. Comput. Chem.
Gaoqi He, Yiping Song, Wenhao Wei, Xia Wang, Xingjian Lu, Honglin Li
2017 J jnl
PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database.
Nucleic Acids Res.
Xia Wang, Yihang Shen, Shiwei Wang, Shiliang Li, Weilin Zhang, Xiaofeng Liu, Luhua Lai, Jianfeng Pei, Honglin Li
2017 J jnl
Statistical Analysis, Investigation, and Prediction of the Water Positions in the Binding Sites of Proteins.
J. Chem. Inf. Model.
Wei Xiao, Zenghui He, Meijian Sun, Shiliang Li, Honglin Li
2016 J jnl
Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors.
BMC Bioinform.
Meijian Sun, Xia Wang, Chuanxin Zou, Zenghui He, Wei Liu, Honglin Li
2016 J jnl
Enhancing the Enrichment of Pharmacophore-Based Target Prediction for the Polypharmacological Profiles of Drugs.
J. Chem. Inf. Model.
Xia Wang, Chenxu Pan, Jiayu Gong, Xiaofeng Liu, Honglin Li
2015 J jnl
An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy.
J. Chem. Inf. Model.
Fang Bai, Sha Liao, Junfeng Gu, Hualiang Jiang, Xicheng Wang, Honglin Li
2014 J jnl
iDrug: a web-accessible and interactive drug discovery and design platform.
J. Cheminformatics
Xia Wang, Haipeng Chen, Feng Yang, Jiayu Gong, Shiliang Li, Jianfeng Pei, Xiaofeng Liu, Hualiang Jiang, Luhua Lai, Honglin Li
2013 J jnl
An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis.
BMC Bioinform.
Chuanxin Zou, Jiayu Gong, Honglin Li
2013 J jnl
ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method.
Bioinform.
Jiayu Gong, Chaoqian Cai, Xiaofeng Liu, Xin Ku, Hualiang Jiang, Daqi Gao, Honglin Li
2013 J jnl
PTID: an integrated web resource and computational tool for agrochemical discovery.
Bioinform.
Jiayu Gong, Xiaofeng Liu, Xianwen Cao, Yanyan Diao, Daqi Gao, Honglin Li, Xuhong Qian
2013 J jnl
SimG: An Alignment Based Method for Evaluating the Similarity of Small Molecules and Binding Sites.
J. Chem. Inf. Model.
Chaoqian Cai, Jiayu Gong, Xiaofeng Liu, Daqi Gao, Honglin Li
2011 J jnl
Identification of Inhibitors against p90 Ribosomal S6 Kinase 2 (RSK2) through Structure-Based Virtual Screening with the Inhibitor-Constrained Refined Homology Model.
J. Chem. Inf. Model.
Shiliang Li, Yi Zhou, Weiqiang Lu, Ye Zhong, Wenlong Song, Kangdong Liu, Jin Huang, Zhenjiang Zhao, Yufang Xu, Xiaofeng Liu, Honglin Li
2011 J jnl
SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening.
J. Chem. Inf. Model.
Xiaofeng Liu, Hualiang Jiang, Honglin Li
2010 J jnl
Bioactive Conformational Generation of Small Molecules: A Comparative Analysis between Force-Field and Multiple Empirical Criteria Based Methods.
BMC Bioinform.
Fang Bai, Xiaofeng Liu, Jiabo Li, Haoyun Zhang, Hualiang Jiang, Xicheng Wang, Honglin Li
2010 J jnl
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach.
Nucleic Acids Res.
Xiaofeng Liu, Sisheng Ouyang, Biao Yu, Yabo Liu, Kai Huang, Jiayu Gong, Siyuan Zheng, Zhihua Li, Honglin Li, Hualiang Jiang
2009 J jnl
An effective docking strategy for virtual screening based on multi-objective optimization algorithm.
BMC Bioinform.
Honglin Li, Hailei Zhang, Mingyue Zheng, Jie Luo, Ling Kang, Xiaofeng Liu, Xicheng Wang, Hualiang Jiang
2009 J jnl
An improved adaptive genetic algorithm for protein-ligand docking.
J. Comput. Aided Mol. Des.
Ling Kang, Honglin Li, Hualiang Jiang, Xicheng Wang
2009 J jnl
Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation.
BMC Bioinform.
Xiaofeng Liu, Fang Bai, Sisheng Ouyang, Xicheng Wang, Honglin Li, Hualiang Jiang
2009 J jnl
Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function.
J. Comput. Biol.
Junfeng Gu, Honglin Li, Hualiang Jiang, Xicheng Wang
2008 J jnl
An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA.
J. Chem. Inf. Model.
Xiaoyu Zhao, Xiaofeng Liu, Yuanyuan Wang, Zhi Chen, Ling Kang, Hailei Zhang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Honglin Li, Xicheng Wang, Hualiang Jiang
2008 J jnl
Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor.
PLoS Comput. Biol.
Xinli Liu, Yechun Xu, Honglin Li, Xicheng Wang, Hualiang Jiang, Francisco J. Barrantes
2008 J jnl
PDTD: a web-accessible protein database for drug target identification.
BMC Bioinform.
Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang, Hualiang Jiang
2006 J jnl
TarFisDock: a web server for identifying drug targets with docking approach.
Nucleic Acids Res.
Honglin Li, Zhenting Gao, Ling Kang, Hailei Zhang, Kun Yang, Kunqian Yu, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Jianhua Shen, Xicheng Wang, Hualiang Jiang