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Gaoqi Weng, Chao Shen, Dongsheng Cao, Junbo Gao, Xiaowu Dong, Qiaojun He, Bo Yang, Dan Li*, Jian Wu*, Tingjun Hou*, PROTAC-DB: an online database of PROTACs, Nucleic Acids Research, 2021, 49(D1), D1381-D1387.
Hongyan Du, Junbo Gao, Gaoqi Weng, Junjie Ding, Xin Chai, Jinping Pang, Yu Kang, Dan Li, Dongsheng Cao*, Tingjun Hou*, CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors, Nucleic Acids Research, 2021, 49(D1), D1122-D1129.
Qing Ye, Xin Chai, Dejun Jiang, Liu Yang, Chao Shen, Xujun Zhang, Dan Li*, Dongsheng Cao*, Tingjun Hou*, Identification of Active Molecules against Mycobacterium Tuberculosis through Machine Learning, Briefings in Bioinformatics, 2021, accepted.
Zhenxing Wu, Dejun Jiang, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Dongsheng Cao*, Tingjun Hou*, Hyperbolic Relational Graph Convolution Networks Plus: a Simple but Highly Efficient QSAR-modeling Method, Briefings in Bioinformatics, 2021, accepted.
Jin-ping Pang, Chao Shen, Wen-fang Zhou, Yunxia Wang, Luhu Shan, Xin Chai, Ying Shao, Xueping Hu, Feng Zhu, Danyan Zhu, Li Xiao, Lei Xu, Xiaohong Xu, Dan Li*, Tingjun Hou*, Discovery of novel antagonists targeting the DNA binding domain of androgen receptor by integrated docking-based virtual screening and bioassays, Acta Pharmacologica Sinica, 2021, accepted.
Ziyi Yang, Zhijiang Yang, Yue Zhao, Mingzhu Yin, Aiping Lu, Xiang Chen, Shao Liu, Tingjun Hou*, Dongsheng Cao*, PySmash: Python package and individual executable program for representative substructure generation and application, Briefings in Bioinformatics, 2021, in press.
Yuan Wang, ZheWang, Jiacheng Liu, Yunwen Wang, Rui Wu, Rong Sheng*, Tingjun Hou*, Discovery of novel HBV capsid assembly modulators by structure-based virtual screening and bioassays, Bioorganic & Medicinal Chemistry, 2021, 36, 116096.
Dejun Jiang, Zhenxing Wu, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Zhe Wang, Chao Shen, Dongsheng Cao*, Jian Wu*, Tingjun Hou*, Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models, Journal of Cheminformatics, 2021, 13, 12.
Xujun Zhang, Chao Shen, Xueying Guo, Zhe Wang, Gaoqi Weng, Qing Ye, Gaoang Wang, Qiaojun He, Bo Yang*, Dongsheng Cao*, Tingjun Hou*, ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions, Journal of Cheminformaticse, 2021, 13, 6.
Ziyi Yang, Zhijiang Yang, Junhong He, Aiping Lu, Shao Liu, Tingjun Hou*, Dongsheng Cao*, Benchmarking the mechanisms of frequent hitters: limitation of PAINS alerts, Drug Discovery Today, 2021, in press.
Li Fu, Ziyi Yang, Zhijiang Yang, Mingzhu Yin, Aiping Lu, Xiang Chen, Shao Liu, Tingjun Hou*, Dongsheng Cao*, QSAR-assisted-MMPA to expand chemical transformation space for lead optimization, Briefings in Bioinformatics, 2021, in press.
Chao Shen, Gaoqi Weng, Xujun Zhang, Elaine Lai-Han Leung, Xiaojun Yao, Jinping Pang, Xin Chai, Dan Li, Ercheng Wang, Dongsheng Cao*, Tingjun Hou*, Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?, Briefings in Bioinformatics, 2021, in press.
Zhenxing Wu, Minfeng Zhu, Yu Kang, Elaine Lai-Han Leung, Tailong Lei, Chao Shen, Dejun Jiang, Zhe Wang, Dongsheng Cao*, Tingjun Hou*, Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets, Briefings in Bioinformatics, 2021, in press.
Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Haiyang Zhong, Gaoang Wang, Xiaojun Yao, Lei Xu, Dongsheng Cao*, Tingjun Hou*, Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions Briefings in Bioinformatics,2021, 22, 497-514.
Jingyu Zhu, Kan Li, Li Yu, Yun Chen, Yanfei Cai, Jian Jin*, Tingjun Hou*, Targeting phosphatidylinositol 3‐kinase gamma (PI3Kγ): Discovery and development of its selective inhibitors, Medicinal Research Reviews, 2021, in press.
Ziyi Yang, Jie Dong, Zhijiang Yang, Mingzhu Yin, Hongli Jiang, Aiping Lu, Xiang Chen, Tingjun Hou*, Dongsheng Cao*, ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds, Briefings in Bioinformatics, 2021, in press.
Jie Dong, Minfeng Zhu, Yonghuan Yun, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, BioMedR: An R/CRAN Package for Integrated Data Analysis Pipeline in Biomedical Study, Briefings in Bioinformatics, 2021, in press.
Ziyi Yang, Zhijiang Yang, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Scopy: an integrated negative design python library for desirable HTS/VS database design, Briefings in Bioinformatics, 2021, in press.
Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Jinping Pang, Gaoang Wang, Haiyang Zhong, Lei Xu, Dongsheng Cao*, Tingjun Hou*, Beware of the generic machine learning-based scoring functions in structure-based virtual screening, Briefings in Bioinformatics, 2021, in press.
Guoli Xiong, Wenling Ye, Chao Shen, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Improving Structure-Based Virtual Screening Performance via Learning from Scoring Function Components, Briefings in Bioinformatics, 2021, in press.
Jike Wang, Dongsheng Cao, Cunchen Tang, Lei Xu, Qiaojun He, Bo Yang, Xi Chen, Huiyong Sun, Tingjun Hou, DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges, Briefings in Bioinformatics, 2021, in press.
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