Dan Li

28 papers Journal 28
YearRankTypeTitle / Venue / Authors
2025 J jnl
ADMET evaluation in drug discovery: 21. Application and industrial validation of machine learning algorithms for Caco-2 permeability prediction.
J. Cheminformatics
Dong Wang, Jieyu Jin, Guqin Shi, Jingxiao Bao, Zheng Wang, Shimeng Li, Peichen Pan, Dan Li, Yu Kang, Tingjun Hou
2025 J jnl
Deep lead optimization enveloped in protein pocket and its application in designing potent and selective ligands targeting LTK protein.
Nat. Mac. Intell.
Shicheng Chen, Odin Zhang, Chenran Jiang, Huifeng Zhao, Xujun Zhang, Mengting Chen, Yun Liu, Qun Su, Zhenxing Wu, Xinyue Wang, Wanglin Qu, Yuanyi Ye, Xin Chai, Ning Wang, Tianyue Wang, Yuan An, Guanlin Wu, Qianqian Yang, Jiean Chen, Wei Xie, Haitao Lin, Dan Li, Chang-Yu Hsieh, Yong Huang, Yu Kang, Tingjun Hou, Peichen Pan
2025 J jnl
Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation.
J. Chem. Inf. Model.
Dou Nie, Huifeng Zhao, Odin Zhang, Gaoqi Weng, Hui Zhang, Jieyu Jin, Haitao Lin, Yufei Huang, Liwei Liu, Dan Li, Tingjun Hou, Yu Kang
2024 J jnl
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space.
J. Chem. Inf. Model.
Mingyang Wang, Zhengjian Wu, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Xiaojun Yao, Zhitong Bing, Chang-Yu Hsieh, Tingjun Hou
2023 J jnl
ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions.
Briefings Bioinform.
Xujun Zhang, Chao Shen, Tianyue Wang, Yafeng Deng, Yu Kang, Dan Li, Tingjun Hou, Peichen Pan
2023 J jnl
PROTAC-DB 2.0: an updated database of PROTACs.
Nucleic Acids Res.
Gaoqi Weng, Xuanyan Cai, Dong-Sheng Cao, Hongyan Du, Chao Shen, Yafeng Deng, Qiaojun He, Bo Yang, Dan Li, Tingjun Hou
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
2021 J jnl
Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?
Briefings Bioinform.
Chao Shen, Gaoqi Weng, Xujun Zhang, Elaine Lai-Han Leung, Xiaojun Yao, Jinping Pang, Xin Chai, Dan Li, Ercheng Wang, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors.
Nucleic Acids Res.
Hongyan Du, Junbo Gao, Gaoqi Weng, Jun-Jie Ding, Xin Chai, Jinping Pang, Yu Kang, Dan Li, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
Identification of active molecules against Mycobacterium tuberculosis through machine learning.
Briefings Bioinform.
Qing Ye, Xin Chai, Dejun Jiang, Liu Yang, Chao Shen, Xujun Zhang, Dan Li, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
PROTAC-DB: an online database of PROTACs.
Nucleic Acids Res.
Gaoqi Weng, Chao Shen, Dong-Sheng Cao, Junbo Gao, Xiaowu Dong, Qiaojun He, Bo Yang, Dan Li, Jian Wu, Tingjun Hou
2020 J jnl
Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power.
Briefings Bioinform.
Chao Shen, Zhe Wang, Xiaojun Yao, Youyong Li, Tailong Lei, Ercheng Wang, Lei Xu, Feng Zhu, Dan Li, Tingjun Hou
2019 J jnl
Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Ye Jin, Mojie Duan, Xuwen Wang, Xiaotian Kong, Wenfang Zhou, Huiyong Sun, Hui Liu, Dan Li, Huidong Yu, Youyong Li, Tingjun Hou
2019 J jnl
HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.
Nucleic Acids Res.
Gaoqi Weng, Ercheng Wang, Zhe Wang, Hui Liu, Feng Zhu, Dan Li, Tingjun Hou
2019 J jnl
farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods.
Bioinform.
Zhe Wang, Xuwen Wang, Youyong Li, Tailong Lei, Ercheng Wang, Dan Li, Yu Kang, Feng Zhu, Tingjun Hou
2018 J jnl
Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products.
J. Chem. Inf. Model.
Jun Shang, Ben Hu, Junmei Wang, Feng Zhu, Yu Kang, Dan Li, Huiyong Sun, De-Xin Kong, Tingjun Hou
2018 J jnl
Discovery of Novel Androgen Receptor Ligands by Structure-based Virtual Screening and Bioassays.
Genom. Proteom. Bioinform.
Wenfang Zhou, Mojie Duan, Weitao Fu, Jinping Pang, Qin Tang, Huiyong Sun, Lei Xu, Shan Chang, Dan Li, Tingjun Hou
2018 J jnl
Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator.
J. Chem. Inf. Model.
Na Liu, Wenfang Zhou, Yue Guo, Junmei Wang, Weitao Fu, Huiyong Sun, Dan Li, Mojie Duan, Tingjun Hou
2017 J jnl
Characterizing Drug-Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches.
J. Chem. Inf. Model.
Huiyong Sun, Youyong Li, Mingyun Shen, Dan Li, Yu Kang, Tingjun Hou
2017 J jnl
Comparative analyses of structural features and scaffold diversity for purchasable compound libraries.
J. Cheminformatics
Jun Shang, Huiyong Sun, Hui Liu, Fu Chen, Sheng Tian, Peichen Pan, Dan Li, De-Xin Kong, Tingjun Hou
2017 J jnl
HawkRank: a new scoring function for protein-protein docking based on weighted energy terms.
J. Cheminformatics
Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu, Tingjun Hou
2016 J jnl
ADMET evaluation in drug discovery: 15. Accurate prediction of rat oral acute toxicity using relevance vector machine and consensus modeling.
J. Cheminformatics
Tailong Lei, Youyong Li, Yunlong Song, Dan Li, Huiyong Sun, Tingjun Hou
2015 J jnl
Identification and Preliminary SAR Analysis of Novel Type-I Inhibitors of TIE-2 via Structure-Based Virtual Screening and Biological Evaluation in in vitro Models.
J. Chem. Inf. Model.
Peichen Pan, Sheng Tian, Huiyong Sun, Xiaotian Kong, Wenfang Zhou, Dan Li, Youyong Li, Tingjun Hou
2015 J jnl
Structure-Activity Relationships and Anti-inflammatory Activities of
J. Chem. Inf. Model.
Yu Zhang, Lei Xu, Zhiqiang Zhang, Zhiyu Zhang, Longtai Zheng, Dan Li, Youyong Li, Feng Liu, Kunqian Yu, Tingjun Hou, Xuechu Zhen
2014 J jnl
Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility.
J. Chem. Inf. Model.
Sheng Tian, Huiyong Sun, Peichen Pan, Dan Li, Xuechu Zhen, Youyong Li, Tingjun Hou
2013 J jnl
Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures.
J. Chem. Inf. Model.
Sheng Tian, Huiyong Sun, Youyong Li, Peichen Pan, Dan Li, Tingjun Hou
2013 J jnl
Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches.
J. Chem. Inf. Model.
Huiyong Sun, Youyong Li, Dan Li, Tingjun Hou
2013 J jnl
Modeling Compound-Target Interaction Network of Traditional Chinese Medicines for Type II Diabetes Mellitus: Insight for Polypharmacology and Drug Design.
J. Chem. Inf. Model.
Sheng Tian, Youyong Li, Dan Li, Xiaojie Xu, Junmei Wang, Qian Zhang, Tingjun Hou