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ORCIDHonglin Li 0003
Person information
- unicode name: 李洪林
- affiliation: East China University of Science and Technology, Key Laboratory of New Drug Design, Shanghai, China
Other persons with the same name
- Honglin Li — disambiguation page
- Honglin Li 0001 — Zhejiang University, College of Computer Science and Technology, China (and 1 more)
- Larry Hong-lin Li (aka: Honglin Li 0002) — National Taiwan University of Arts, General Education Center, New Taipei City, Taiwan
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2020 – today
- 2024
[j42]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:
MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. Briefings Bioinform. 25(2) (2024)- [j41]Zijing Tian, Yan Dai, Feng Hu, Zihao Shen, Hongling Xu, Hongwen Zhang, Jinhang Xu, Yuting Hu, Yanyan Diao, Honglin Li:
Enhancing Chemical Reaction Monitoring with a Deep Learning Model for NMR Spectra Image Matching to Target Compounds. J. Chem. Inf. Model. 64(14): 5624-5633 (2024) - [j40]Kai Zhang, Junchen Shen, Gaoqi He, Yu Sun, Haibin Ling, Hongyuan Zha, Honglin Li, Jie Zhang:
A Transformative Topological Representation for Link Modeling, Prediction and Cross-Domain Network Analysis. IEEE Trans. Pattern Anal. Mach. Intell. 46(9): 6126-6138 (2024) - 2023
- [j39]Yanyan Diao, Feng Hu, Zihao Shen, Honglin Li:
MacFrag: segmenting large-scale molecules to obtain diverse fragments with high qualities. Bioinform. 39(1) (2023) - [j38]Yunxia Wang, Zhen Chen, Ziqi Pan, Shijie Huang, Jin Liu, Weiqi Xia, Hongning Zhang, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu:
RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction. Nucleic Acids Res. 51(W1): 509-519 (2023) - 2022
- [j37]Mingyang Wang, Huiyong Sun, Jike Wang, Jinping Pang, Xin Chai, Lei Xu, Honglin Li, Dongsheng Cao, Tingjun Hou:
Comprehensive assessment of deep generative architectures for de novo drug design. Briefings Bioinform. 23(1) (2022) - [j36]Ziyan Feng, Zihao Shen, Honglin Li, Shiliang Li:
e-TSN: an interactive visual exploration platform for target-disease knowledge mapping from literature. Briefings Bioinform. 23(6) (2022) - [j35]Jie Wang, Zihao Shen, Yichen Liao, Zhen Yuan, Shiliang Li, Gaoqi He, Man Lan, Xuhong Qian, Kai Zhang, Honglin Li:
Multi-modal chemical information reconstruction from images and texts for exploring the near-drug space. Briefings Bioinform. 23(6) (2022) - [j34]Hanyu Zhang, Yunxia Wang, Ziqi Pan, Xiuna Sun, Minjie Mou, Bing Zhang, Zhaorong Li, Honglin Li, Feng Zhu:
ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA. Briefings Bioinform. 23(6) (2022) - [j33]Shun Liu, Jianchao Zhou, Ziyan Feng, Jiawen Zhang, Shuang Li, Zilong Jin, Chenfei Zhang, Shiliang Li, Gaoqi He, Honglin Li:
VRPharmer: bringing virtual reality into pharmacophore-based virtual screening with interactive exploration and realistic visualization. Bioinform. 38(21): 4953-4955 (2022) - [j32]Weiqi Xia, Lingyan Zheng, Jiebin Fang, Fengcheng Li, Ying Zhou, Zhenyu Zeng, Bing Zhang, Zhaorong Li, Honglin Li, Feng Zhu:
PFmulDL: a novel strategy enabling multi-class and multi-label protein function annotation by integrating diverse deep learning methods. Comput. Biol. Medicine 145: 105465 (2022) - [j31]Zhanpeng Xu, Jianhua Li, Zhaopeng Yang, Shiliang Li, Honglin Li:
SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer. J. Cheminformatics 14(1): 41 (2022) - [j30]Mingyang Wang, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Honglin Li, Chang-Yu Hsieh, Tingjun Hou:
ReMODE: a deep learning-based web server for target-specific drug design. J. Cheminformatics 14(1): 84 (2022) - [j29]Jianhua Li, Guanlong Liu, Zhiyuan Zhen, Zihao Shen, Shiliang Li, Honglin Li:
Molecular Docking for Ligand-Receptor Binding Process Based on Heterogeneous Computing. Sci. Program. 2022: 9197606:1-9197606:13 (2022) - 2021
- [j28]Yuxia Mao, Shiliang Li, Bojie Gong, Luhua Lai, Gaoqi He, Honglin Li:
ePharmer: An integrated and graphical software for pharmacophore-based virtual screening. J. Comput. Chem. 42(30): 2181-2195 (2021) - [j27]Yuxia Mao, Shiliang Li, Bojie Gong, Luhua Lai, Gaoqi He, Honglin Li:
Cover Image. J. Comput. Chem. 42(30): i (2021) - 2020
- [j26]Yue Chen, Junhao Li, Zengrui Wu, Guixia Liu, Honglin Li, Yun Tang, Weihua Li:
Computational Insight into the Allosteric Activation Mechanism of Farnesoid X Receptor. J. Chem. Inf. Model. 60(3): 1540-1550 (2020) - [j25]Qingxia Yang, Yunxia Wang, Ying Zhang, Fengcheng Li, Weiqi Xia, Ying Zhou, Yunqing Qiu, Honglin Li, Feng Zhu:
NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data. Nucleic Acids Res. 48(Webserver-Issue): W436-W448 (2020)
2010 – 2019
- 2019
- [j24]Gaoqi He, Yiping Song, Wenhao Wei, Xia Wang, Xingjian Lu, Honglin Li:
eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity. J. Comput. Chem. 40(6): 826-838 (2019) - [j23]Wen Yang, Xia Wang, Kenan Li, Yuanru Liu, Ying Liu, Rui Wang, Honglin Li:
Pharmacodynamics simulation of HOEC by a computational model of arachidonic acid metabolic network. Quant. Biol. 7(1): 30-41 (2019) - 2017
- [j22]Wei Xiao, Zenghui He, Meijian Sun, Shiliang Li, Honglin Li:
Statistical Analysis, Investigation, and Prediction of the Water Positions in the Binding Sites of Proteins. J. Chem. Inf. Model. 57(7): 1517-1528 (2017) - [j21]Xia Wang, Yihang Shen, Shiwei Wang, Shiliang Li, Weilin Zhang, Xiaofeng Liu, Luhua Lai, Jianfeng Pei, Honglin Li:
PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database. Nucleic Acids Res. 45(Webserver-Issue): W356-W360 (2017) - 2016
- [j20]Meijian Sun, Xia Wang, Chuanxin Zou, Zenghui He, Wei Liu, Honglin Li:
Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors. BMC Bioinform. 17: 231 (2016) - [j19]Xia Wang, Chenxu Pan, Jiayu Gong, Xiaofeng Liu, Honglin Li:
Enhancing the Enrichment of Pharmacophore-Based Target Prediction for the Polypharmacological Profiles of Drugs. J. Chem. Inf. Model. 56(6): 1175-1183 (2016) - 2015
- [j18]Fang Bai, Sha Liao, Junfeng Gu, Hualiang Jiang, Xicheng Wang, Honglin Li:
An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy. J. Chem. Inf. Model. 55(4): 833-847 (2015) - 2014
- [j17]Xia Wang, Haipeng Chen, Feng Yang, Jiayu Gong, Shiliang Li, Jianfeng Pei, Xiaofeng Liu, Hualiang Jiang, Luhua Lai, Honglin Li:
iDrug: a web-accessible and interactive drug discovery and design platform. J. Cheminformatics 6(1): 28 (2014) - 2013
- [j16]Jiayu Gong, Xiaofeng Liu, Xianwen Cao, Yanyan Diao, Daqi Gao, Honglin Li, Xuhong Qian:
PTID: an integrated web resource and computational tool for agrochemical discovery. Bioinform. 29(2): 292-294 (2013) - [j15]Jiayu Gong, Chaoqian Cai, Xiaofeng Liu, Xin Ku, Hualiang Jiang, Daqi Gao, Honglin Li:
ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method. Bioinform. 29(14): 1827-1829 (2013) - [j14]Chuanxin Zou, Jiayu Gong, Honglin Li:
An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis. BMC Bioinform. 14: 90 (2013) - [j13]Chaoqian Cai, Jiayu Gong, Xiaofeng Liu, Daqi Gao, Honglin Li:
SimG: An Alignment Based Method for Evaluating the Similarity of Small Molecules and Binding Sites. J. Chem. Inf. Model. 53(8): 2103-2115 (2013) - 2011
- [j12]Xiaofeng Liu, Hualiang Jiang, Honglin Li:
SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening. J. Chem. Inf. Model. 51(9): 2372-2385 (2011) - [j11]Shiliang Li, Yi Zhou, Weiqiang Lu, Ye Zhong, Wenlong Song, Kangdong Liu, Jin Huang, Zhenjiang Zhao, Yufang Xu, Xiaofeng Liu, Honglin Li:
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. 51(11): 2939-2947 (2011) - 2010
- [j10]Fang Bai, Xiaofeng Liu, Jiabo Li, Haoyun Zhang, Hualiang Jiang, Xicheng Wang, Honglin Li:
Bioactive Conformational Generation of Small Molecules: A Comparative Analysis between Force-Field and Multiple Empirical Criteria Based Methods. BMC Bioinform. 11: 545 (2010) - [j9]Xiaofeng Liu, Sisheng Ouyang, Biao Yu, Yabo Liu, Kai Huang, Jiayu Gong, Siyuan Zheng, Zhihua Li, Honglin Li, Hualiang Jiang:
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. Nucleic Acids Res. 38(Web-Server-Issue): 609-614 (2010)
2000 – 2009
- 2009
- [j8]Honglin Li, Hailei Zhang, Mingyue Zheng, Jie Luo, Ling Kang, Xiaofeng Liu, Xicheng Wang, Hualiang Jiang:
An effective docking strategy for virtual screening based on multi-objective optimization algorithm. BMC Bioinform. 10 (2009) - [j7]Xiaofeng Liu, Fang Bai, Sisheng Ouyang, Xicheng Wang, Honglin Li, Hualiang Jiang:
Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation. BMC Bioinform. 10 (2009) - [j6]Ling Kang, Honglin Li, Hualiang Jiang, Xicheng Wang:
An improved adaptive genetic algorithm for protein-ligand docking. J. Comput. Aided Mol. Des. 23(1): 1-12 (2009) - [j5]Junfeng Gu, Honglin Li, Hualiang Jiang, Xicheng Wang:
Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function. J. Comput. Biol. 16(3): 427-442 (2009) - 2008
- [j4]Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang, Hualiang Jiang:
PDTD: a web-accessible protein database for drug target identification. BMC Bioinform. 9 (2008) - [j3]Xiaoyu Zhao, Xiaofeng Liu, Yuanyuan Wang, Zhi Chen, Ling Kang, Hailei Zhang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Honglin Li, Xicheng Wang, Hualiang Jiang:
An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA. J. Chem. Inf. Model. 48(7): 1438-1447 (2008) - [j2]Xinli Liu, Yechun Xu, Honglin Li, Xicheng Wang, Hualiang Jiang, Francisco J. Barrantes:
Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor. PLoS Comput. Biol. 4(1) (2008) - 2006
- [j1]Honglin Li, Zhenting Gao, Ling Kang, Hailei Zhang, Kun Yang, Kunqian Yu, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Jianhua Shen, Xicheng Wang, Hualiang Jiang:
TarFisDock: a web server for identifying drug targets with docking approach. Nucleic Acids Res. 34(Web-Server-Issue): 219-224 (2006)
Coauthor Index
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