Tingjun Hou

ORCID

Publication Activity (10 Years)

Years Active: 1999-2024
Publications (10 Years): 115

Top Venues

Publications

Jike Wang, Rui Qin, Mingyang Wang, Meijing Fang, Yangyang Zhang, Yuchen Zhu, Qun Su, Qiaolin Gou, Chao Shen, Odin Zhang, Zhenxing Wu, Dejun Jiang, Xujun Zhang, Huifeng Zhao, Xiaozhe Wan, Zhourui Wu, Liwei Liu, Yu Kang, Chang-Yu Hsieh, Tingjun Hou
Token-Mol 1.0: Tokenized drug design with large language model. CoRR (2024)
Tianhao Wang, Jianbo Tong, Xing Zhang, Zhe Wang, Lei Xu, Peichen Pan, Tingjun Hou
Structure-based virtual screening of novel USP5 inhibitors targeting the zinc finger ubiquitin-binding domain. Comput. Biol. Medicine 174 (2024)
Huifeng Zhao, Dejun Jiang, Chao Shen, Jintu Zhang, Xujun Zhang, Xiaorui Wang, Dou Nie, Tingjun Hou, Yu Kang
Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes. J. Chem. Inf. Model. 64 (6) (2024)
Lijun Liu, Jiali Yang, Jianfei Song, Xinglin Yang, Lele Niu, Zeqi Cai, Hui Shi, Tingjun Hou, Chang-Yu Hsieh, Weiran Shen, Yafeng Deng
AAVDiff: Experimental Validation of Enhanced Viability and Diversity in Recombinant Adeno-Associated Virus (AAV) Capsids through Diffusion Generation. CoRR (2024)
Odin Zhang, Haitao Lin, Hui Zhang, Huifeng Zhao, Yufei Huang, Yuansheng Huang, Dejun Jiang, Chang-Yu Hsieh, Peichen Pan, Tingjun Hou
Deep Lead Optimization: Leveraging Generative AI for Structural Modification. CoRR (2024)
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
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. 64 (4) (2024)
Ruofan Jin, Qing Ye, Jike Wang, Zheng Cao, Dejun Jiang, Tianyue Wang, Yu Kang, Wanting Xu, Chang-Yu Hsieh, Tingjun Hou
AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences. Briefings Bioinform. 25 (4) (2024)
Yiheng Zhu, Zitai Kong, Jialu Wu, Weize Liu, Yuqiang Han, Mingze Yin, Hongxia Xu, Chang-Yu Hsieh, Tingjun Hou
Generative AI for Controllable Protein Sequence Design: A Survey. CoRR (2024)
Xing Zhang, Jianbo Tong, Tianhao Wang, Tianyue Wang, Lei Xu, Zhe Wang, Tingjun Hou, Peichen Pan
Dissecting the role of ALK double mutations in drug resistance to lorlatinib with in-depth theoretical modeling and analysis. Comput. Biol. Medicine 169 (2024)
Mingze Yin, Hanjing Zhou, Yiheng Zhu, Miao Lin, Yixuan Wu, Jialu Wu, Hongxia Xu, Chang-Yu Hsieh, Tingjun Hou, Jintai Chen, Jian Wu
Multi-Modal CLIP-Informed Protein Editing. CoRR (2024)
Nanqi Hong, Dejun Jiang, Zhe Wang, Huiyong Sun, Hao Luo, Lingjie Bao, Mingli Song, Yu Kang, Tingjun Hou
TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides. J. Chem. Inf. Model. 64 (13) (2024)
Wenjia Qian, Xiaorui Wang, Yu Kang, Peichen Pan, Tingjun Hou, Chang-Yu Hsieh
A general model for predicting enzyme functions based on enzymatic reactions. J. Cheminformatics 16 (1) (2024)
Odin Zhang, Yufei Huang, Shichen Cheng, Mengyao Yu, Xujun Zhang, Haitao Lin, Yundian Zeng, Mingyang Wang, Zhenxing Wu, Huifeng Zhao, Zaixi Zhang, Chenqing Hua, Yu Kang, Sunliang Cui, Peichen Pan, Chang-Yu Hsieh, Tingjun Hou
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation. CoRR (2024)
Chao Shen, Jianfei Song, Chang-Yu Hsieh, Dong-Sheng Cao, Yu Kang, Wenling Ye, Zhenxing Wu, Jike Wang, Odin Zhang, Xujun Zhang, Hao Zeng, Heng Cai, Yu Chen, Linkang Chen, Hao Luo, Xinda Zhao, Tianye Jian, Tong Chen, Dejun Jiang, Mingyang Wang, Qing Ye, Jialu Wu, Hongyan Du, Hui Shi, Yafeng Deng, Tingjun Hou
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery. J. Chem. Inf. Model. 64 (14) (2024)
Shukai Gu, Yuwei Yang, Yihao Zhao, Jiayue Qiu, Xiaorui Wang, Henry Hoi Yee Tong, Liwei Liu, Xiaozhe Wan, Huanxiang Liu, Tingjun Hou, Yu Kang
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. J. Chem. Inf. Model. 64 (9) (2024)
Odin Zhang, Tianyue Wang, Gaoqi Weng, Dejun Jiang, Ning Wang, Xiaorui Wang, Huifeng Zhao, Jialu Wu, Ercheng Wang, Guangyong Chen, Yafeng Deng, Peichen Pan, Yu Kang, Chang-Yu Hsieh, Tingjun Hou
Learning on topological surface and geometric structure for 3D molecular generation. Nat. Comput. Sci. 3 (10) (2023)
Xujun Zhang, Chao Shen, Tianyue Wang, Yafeng Deng, Yu Kang, Dan Li, Tingjun Hou, Peichen Pan
ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions. Briefings Bioinform. 24 (5) (2023)
Jintu Zhang, Haotian Zhang, Zhixin Qin, Yu Kang, Xin Hong, Tingjun Hou
Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials. J. Chem. Inf. Model. 63 (4) (2023)
Dong Wang, Zhenxing Wu, Chao Shen, Lingjie Bao, Hao Luo, Zhe Wang, Hucheng Yao, De-Xin Kong, Cheng Luo, Tingjun Hou
Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors. Briefings Bioinform. 24 (1) (2023)
Yuchen Sun, Xibing He, Tingjun Hou, Lianjin Cai, Viet Hoang Man, Junmei Wang
Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method. J. Comput. Chem. 44 (14) (2023)
Gaoqi Weng, Xuanyan Cai, Dong-Sheng Cao, Hongyan Du, Chao Shen, Yafeng Deng, Qiaojun He, Bo Yang, Dan Li, Tingjun Hou
PROTAC-DB 2.0: an updated database of PROTACs. Nucleic Acids Res. 51 (D1) (2023)
Hongyan Du, Guo-Wei Wei, Tingjun Hou
Multiscale Topology in Interactomic Network: From Transcriptome to Antiaddiction Drug Repurposing. CoRR (2023)
Zhenxing Wu, Jihong Chen, Yitong Li, Yafeng Deng, Haitao Zhao, Chang-Yu Hsieh, Tingjun Hou
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery. J. Chem. Inf. Model. 63 (24) (2023)
Yue Wan, Jialu Wu, Tingjun Hou, Chang-Yu Hsieh, Xiaowei Jia
From molecules to scaffolds to functional groups: building context-dependent molecular representation via multi-channel learning. CoRR (2023)
Yiheng Zhu, Zhenqiu Ouyang, Ben Liao, Jialu Wu, Yixuan Wu, Chang-Yu Hsieh, Tingjun Hou, Jian Wu
MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation. IJCAI (2023)
Haiyi Chen, Yue Guo, Shengqing Ye, Jintu Zhang, Haotian Zhang, Na Liu, Rui Zhou, Tingjun Hou, Hongguang Xia, Yu Kang, Mojie Duan
On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate. J. Chem. Inf. Model. 63 (16) (2023)
Zhe Wang, Haiyang Zhong, Jintu Zhang, Peichen Pan, Dong Wang, Huanxiang Liu, Xiaojun Yao, Tingjun Hou, Yu Kang
Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets. J. Chem. Inf. Model. 63 (21) (2023)
Yanqing Duan, Li Fu, Xiao-Chen Zhang, Teng-Zhi Long, Yuan-Hang He, Zhao-Qian Liu, Ai-Ping Lu, Yafeng Deng, Chang-Yu Hsieh, Tingjun Hou, Dong-Sheng Cao
Prediction by Transferring Knowledge from Low-Fidelity Data. J. Chem. Inf. Model. 63 (8) (2023)
Zipeng Zhong, Jie Song, Zunlei Feng, Tiantao Liu, Lingxiang Jia, Shaolun Yao, Tingjun Hou, Mingli Song
Recent advances in artificial intelligence for retrosynthesis. CoRR (2023)
Lingling Wang, Lei Xu, Zhe Wang, Tingjun Hou, Haiping Hao, Huiyong Sun
Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis. Briefings Bioinform. 24 (1) (2023)
Jike Wang, Yundian Zeng, Huiyong Sun, Junmei Wang, Xiaorui Wang, Ruofan Jin, Mingyang Wang, Xujun Zhang, Dong-Sheng Cao, Xi Chen, Chang-Yu Hsieh, Tingjun Hou
Molecular Generation with Reduced Labeling through Constraint Architecture. J. Chem. Inf. Model. 63 (11) (2023)
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) (2023)
Odin Zhang, Jintu Zhang, Jieyu Jin, Xujun Zhang, Renling Hu, Chao Shen, Hanqun Cao, Hongyan Du, Yu Kang, Yafeng Deng, Furui Liu, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou
ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling. Nat. Mac. Intell. 5 (9) (2023)
Shukai Gu, Chao Shen, Jiahui Yu, Hong Zhao, Huanxiang Liu, Liwei Liu, Rong Sheng, Lei Xu, Zhe Wang, Tingjun Hou, Yu Kang
Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning? Briefings Bioinform. 24 (2) (2023)
Kai-Yue Ji, Chong Liu, Zhao-Qian Liu, Yafeng Deng, Tingjun Hou, Dong-Sheng Cao
Comprehensive assessment of nine target prediction web services: which should we choose for target fishing? Briefings Bioinform. 24 (2) (2023)
Xujun Zhang, Chao Shen, Dejun Jiang, Jintu Zhang, Qing Ye, Lei Xu, Tingjun Hou, Peichen Pan, Yu Kang
TB-IECS: an accurate machine learning-based scoring function for virtual screening. J. Cheminformatics 15 (1) (2023)
Jian Gao, Zheyuan Shen, Yufeng Xie, Jialiang Lu, Yang Lu, Sikang Chen, Qingyu Bian, Yue Guo, Liteng Shen, Jian Wu, Binbin Zhou, Tingjun Hou, Qiaojun He, Jinxin Che, Xiaowu Dong
TransFoxMol: predicting molecular property with focused attention. Briefings Bioinform. 24 (5) (2023)
Xiaodan Yin, Xiaorui Wang, Yuquan Li, Jike Wang, Yuwei Wang, Yafeng Deng, Tingjun Hou, Huanxiang Liu, Pei Luo, Xiaojun Yao
CODD-Pred: A Web Server for Efficient Target Identification and Bioactivity Prediction of Small Molecules. J. Chem. Inf. Model. 63 (20) (2023)
Teng-Zhi Long, Shao-Hua Shi, Shao Liu, Ai-Ping Lu, Zhao-Qian Liu, Min Li, Tingjun Hou, Dong-Sheng Cao
Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. J. Chem. Inf. Model. 63 (1) (2023)
Su-Qing Yang, Liu-Xia Zhang, You-Jin Ge, Jin-Wei Zhang, Jian-Xin Hu, Cheng-Ying Shen, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences. J. Cheminformatics 15 (1) (2023)
Yuchen Sun, Tingjun Hou, Xibing He, Viet Hoang Man, Junmei Wang
-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method. J. Comput. Chem. 44 (13) (2023)
Fengcheng Li, Jiayi Yin, Mingkun Lu, Minjie Mou, Zhaorong Li, Zhenyu Zeng, Ying Tan, Shanshan Wang, Xinyi Chu, Haibin Dai, Tingjun Hou, Su Zeng, Yuzong Chen, Feng Zhu
DrugMAP: molecular atlas and pharma-information of all drugs. Nucleic Acids Res. 51 (D1) (2023)
Sutong Xiang, Zhe Wang, Rongfan Tang, Lingling Wang, Qinghua Wang, Yang Yu, Qirui Deng, Tingjun Hou, Haiping Hao, Huiyong Sun
Combined Enhanced Sampling. J. Chem. Inf. Model. 63 (23) (2023)
Yuwei Yang, Chang-Yu Hsieh, Yu Kang, Tingjun Hou, Huanxiang Liu, Xiaojun Yao
Deep Generation Model Guided by the Docking Score for Active Molecular Design. J. Chem. Inf. Model. 63 (10) (2023)
Yiheng Zhu, Jialu Wu, Chaowen Hu, Jiahuan Yan, Chang-Yu Hsieh, Tingjun Hou, Jian Wu
Sample-efficient Multi-objective Molecular Optimization with GFlowNets. CoRR (2023)
Kuerbannisha Amahong, Wei Zhang, Ying Zhou, Song Zhang, Jiayi Yin, Fengcheng Li, Hong-Quan Xu, Tian-Ci Yan, Zi-Xuan Yue, Yu-Hong Liu, Tingjun Hou, Yunqing Qiu, Lin Tao, Lianyi Han, Feng Zhu
CovInter: interaction data between coronavirus RNAs and host proteins. Nucleic Acids Res. 51 (D1) (2023)
Lei Wang, Shao-Hua Shi, Hui Li, Xiangxiang Zeng, Su-You Liu, Zhao-Qian Liu, Yafeng Deng, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
Reducing false positive rate of docking-based virtual screening by active learning. Briefings Bioinform. 24 (1) (2023)
Kexin Chen, Guangyong Chen, Junyou Li, Yuansheng Huang, Ercheng Wang, Tingjun Hou, Pheng-Ann Heng
MetaRF: attention-based random forest for reaction yield prediction with a few trails. J. Cheminformatics 15 (1) (2023)
Yiheng Zhu, Zhenqiu Ouyang, Ben Liao, Jialu Wu, Yixuan Wu, Chang-Yu Hsieh, Tingjun Hou, Jian Wu
MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation. CoRR (2023)
Yiheng Zhu, Jialu Wu, Chaowen Hu, Jiahuan Yan, kim hsieh, Tingjun Hou, Jian Wu
Sample-efficient Multi-objective Molecular Optimization with GFlowNets. NeurIPS (2023)
Xujun Zhang, Odin Zhang, Chao Shen, Wanglin Qu, Shicheng Chen, Hanqun Cao, Yu Kang, Zhe Wang, Ercheng Wang, Jintu Zhang, Yafeng Deng, Furui Liu, Tianyue Wang, Hongyan Du, Langcheng Wang, Peichen Pan, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou
Efficient and accurate large library ligand docking with KarmaDock. Nat. Comput. Sci. 3 (9) (2023)
Zhe Wang, Hong Pan, Huiyong Sun, Yu Kang, Huanxiang Liu, Dongsheng Cao, Tingjun Hou
fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation. Briefings Bioinform. 23 (5) (2022)
Jiahui Yu, Jike Wang, Hong Zhao, Junbo Gao, Yu Kang, Dong-Sheng Cao, Zhe Wang, Tingjun Hou
Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism. J. Chem. Inf. Model. 62 (12) (2022)
Yuwei Yang, Zhenxing Wu, Xiaojun Yao, Yu Kang, Tingjun Hou, Chang-Yu Hsieh, Huanxiang Liu
Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation. J. Chem. Inf. Model. 62 (13) (2022)
Rongfan Tang, Pengcheng Chen, Zhe Wang, Lingling Wang, Haiping Hao, Tingjun Hou, Huiyong Sun
Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations. Briefings Bioinform. 23 (3) (2022)
Dejun Jiang, Huiyong Sun, Jike Wang, Chang-Yu Hsieh, Yuquan Li, Zhenxing Wu, Dong-Sheng Cao, Jian Wu, Tingjun Hou
Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning. Briefings Bioinform. 23 (2) (2022)
Zipeng Zhong, Jie Song, Zunlei Feng, Tiantao Liu, Lingxiang Jia, Shaolun Yao, Min Wu, Tingjun Hou, Mingli Song
Root-aligned SMILES for Molecular Retrosynthesis Prediction. CoRR (2022)
Yang Yu, Zhe Wang, Lingling Wang, Sheng Tian, Tingjun Hou, Huiyong Sun
Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses. J. Cheminformatics 14 (1) (2022)
Zhenxing Wu, Dejun Jiang, Jike Wang, Xujun Zhang, Hongyan Du, Lurong Pan, Chang-Yu Hsieh, Dongsheng Cao, Tingjun Hou
Knowledge-based BERT: a method to extract molecular features like computational chemists. Briefings Bioinform. 23 (3) (2022)
Qinghua Wang, Zhe Wang, Sheng Tian, Lingling Wang, Rongfan Tang, Yang Yu, Jingxuan Ge, Tingjun Hou, Haiping Hao, Huiyong Sun
Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning. J. Chem. Inf. Model. 62 (17) (2022)
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) (2022)
Haiyi Chen, Rui Zhou, Jinping Pang, Yue Guo, Jiawen Chen, Yu Kang, Mojie Duan, Tingjun Hou
Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands. J. Chem. Inf. Model. 62 (21) (2022)
Jia-Cai Yi, Chengkun Wu, Xiao-Chen Zhang, Xinyi Xiao, Yanlong Qiu, Wentao Zhao, Tingjun Hou, Dong-Sheng Cao
MICER: a pre-trained encoder-decoder architecture for molecular image captioning. Bioinform. 38 (19) (2022)
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)
Xiao-Chen Zhang, Jia-Cai Yi, Guo-Ping Yang, Chengkun Wu, Tingjun Hou, Dong-Sheng Cao
ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images. Briefings Bioinform. 23 (2) (2022)
Guo-Li Xiong, Zhi-Jiang Yang, Jia-Cai Yi, Ningning Wang, Lei Wang, Huimin Zhu, Chengkun Wu, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dongsheng Cao
DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety. Nucleic Acids Res. 50 (D1) (2022)
Gaoang Wang, Jiahui Yu, Hongyan Du, Chao Shen, Xujun Zhang, Yifei Liu, Yangyang Zhang, Dong-Sheng Cao, Peichen Pan, Tingjun Hou
VGSC-DB: an online database of voltage-gated sodium channels. J. Cheminformatics 14 (1) (2022)
Jialu Wu, Junmei Wang, Zhenxing Wu, Shengyu Zhang, Yafeng Deng, Yu Kang, Dong-Sheng Cao, Chang-Yu Hsieh, Tingjun Hou
ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction. J. Chem. Inf. Model. 62 (23) (2022)
Ning-Ning Wang, Xiang-Gui Wang, Guo-Li Xiong, Zi-Yi Yang, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dong-Sheng Cao
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes. J. Cheminformatics 14 (1) (2022)
Ercheng Wang, Weitao Fu, Dejun Jiang, Huiyong Sun, Junmei Wang, Xujun Zhang, Gaoqi Weng, Hui Liu, Peng Tao, Tingjun Hou
VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations. J. Chem. Inf. Model. 61 (6) (2021)
Jike Wang, Dong-Sheng 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 Bioinform. 22 (3) (2021)
Zi-Yi Yang, Li Fu, Ai-Ping Lu, Shao Liu, Tingjun Hou, Dong-Sheng Cao
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion. J. Cheminformatics 13 (1) (2021)
Jike Wang, Huiyong Sun, Jiawen Chen, Dejun Jiang, Zhe Wang, Zhenxing Wu, Xi Chen, Dong-Sheng Cao, Tingjun Hou
machine-learning algorithms. Bioinform. 37 (22) (2021)
Zhenxing Wu, Dejun Jiang, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Dong-Sheng Cao, Tingjun Hou
Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method. Briefings Bioinform. 22 (5) (2021)
Guo-Li Xiong, Zhenxing Wu, Jia-Cai Yi, Li Fu, Zhi-Jiang Yang, Chang-Yu Hsieh, Mingzhu Yin, Xiangxiang Zeng, Chengkun Wu, Ai-Ping Lu, Xiang Chen, Tingjun Hou, Dong-Sheng Cao
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Zi-Yi Yang, Zhi-Jiang Yang, Yue Zhao, Ming-Zhu Yin, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dong-Sheng Cao
PySmash: Python package and individual executable program for representative substructure generation and application. Briefings Bioinform. 22 (5) (2021)
Zi-Yi Yang, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
Scopy: an integrated negative design python library for desirable HTS/VS database design. Briefings Bioinform. 22 (3) (2021)
Xujun Zhang, Chao Shen, Xueying Guo, Zhe Wang, Gaoqi Weng, Qing Ye, Gaoang Wang, Qiaojun He, Bo Yang, Dong-Sheng Cao, Tingjun Hou
ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions. J. Cheminformatics 13 (1) (2021)
Zi-Yi Yang, Jie Dong, Zhi-Jiang Yang, Mingzhu Yin, Hong-Li Jiang, Ai-Ping Lu, Xiang Chen, Tingjun Hou, Dong-Sheng Cao
ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds. Briefings Bioinform. 22 (4) (2021)
Li Fu, Zi-Yi Yang, Zhi-Jiang Yang, Ming-Zhu Yin, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dong-Sheng Cao
QSAR-assisted-MMPA to expand chemical transformation space for lead optimization. Briefings Bioinform. 22 (5) (2021)
Jike Wang, Chang-Yu Hsieh, Mingyang Wang, Xiaorui Wang, Zhenxing Wu, Dejun Jiang, Benben Liao, Xujun Zhang, Bo Yang, Qiaojun He, Dongsheng Cao, Xi Chen, Tingjun Hou
Multi-constraint molecular generation based on conditional transformer, knowledge distillation and reinforcement learning. Nat. Mach. Intell. 3 (10) (2021)
Chengkun Wu, Xiao-Chen Zhang, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules. Briefings Bioinform. 22 (6) (2021)
Qing Ye, Xin Chai, Dejun Jiang, Liu Yang, Chao Shen, Xujun Zhang, Dan Li, Dong-Sheng Cao, Tingjun Hou
Identification of active molecules against Mycobacterium tuberculosis through machine learning. Briefings Bioinform. 22 (5) (2021)
Zhenxing Wu, Minfeng Zhu, Yu Kang, Elaine Lai-Han Leung, Tailong Lei, Chao Shen, Dejun Jiang, Zhe Wang, Dong-Sheng 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 Bioinform. 22 (4) (2021)
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
Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening? Briefings Bioinform. 22 (5) (2021)
Hongyan Du, Junbo Gao, Gaoqi Weng, Jun-Jie Ding, Xin Chai, Jinping Pang, Yu Kang, Dan Li, Dong-Sheng Cao, Tingjun Hou
CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. Nucleic Acids Res. 49 (Database-Issue) (2021)
Gaoqi Weng, Chao Shen, Dong-Sheng Cao, Junbo Gao, Xiaowu Dong, Qiaojun He, Bo Yang, Dan Li, Jian Wu, Tingjun Hou
PROTAC-DB: an online database of PROTACs. Nucleic Acids Res. 49 (Database-Issue) (2021)
Guo-Li Xiong, Wen-Ling Ye, Chao Shen, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
Improving structure-based virtual screening performance via learning from scoring function components. Briefings Bioinform. 22 (3) (2021)
Dejun Jiang, Zhenxing Wu, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Zhe Wang, Chao Shen, Dong-Sheng 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. J. Cheminformatics 13 (1) (2021)
Chao Shen, Xueping Hu, Junbo Gao, Xujun Zhang, Haiyang Zhong, Zhe Wang, Lei Xu, Yu Kang, Dong-Sheng Cao, Tingjun Hou
The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction. J. Cheminformatics 13 (1) (2021)
Xiao-Chen Zhang, Chengkun Wu, Zhi-Jiang Yang, Zhen-Xing Wu, Jia-Cai Yi, Chang-Yu Hsieh, Tingjun Hou, Dong-Sheng Cao
MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction. Briefings Bioinform. 22 (6) (2021)
Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Jinping Pang, Gaoang Wang, Haiyang Zhong, Lei Xu, Dong-Sheng Cao, Tingjun Hou
Beware of the generic machine learning-based scoring functions in structure-based virtual screening. Briefings Bioinform. 22 (3) (2021)
Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Haiyang Zhong, Gaoang Wang, Xiaojun Yao, Lei Xu, Dong-Sheng 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 Bioinform. 22 (1) (2021)
Jie Dong, Min-Feng Zhu, Yong-Huan Yun, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study. Briefings Bioinform. 22 (1) (2021)
Jike Wang, Dong-Sheng Cao, Cunchen Tang, Xi Chen, Huiyong Sun, Tingjun Hou
Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning. Bioinform. 36 (18) (2020)
Wen-Ling Ye, Chao Shen, Guo-Li Xiong, Jun-Jie Ding, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring. J. Chem. Inf. Model. 60 (9) (2020)
Chao Shen, Zhe Wang, Xiaojun Yao, Youyong Li, Tailong Lei, Ercheng Wang, Lei Xu, Feng Zhu, Dan Li, Tingjun Hou
Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. Briefings Bioinform. 21 (1) (2020)
Dejun Jiang, Tailong Lei, Zhe Wang, Chao Shen, Dong-Sheng Cao, Tingjun Hou
ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning. J. Cheminformatics 12 (1) (2020)
Zi-Yi Yang, Jie Dong, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays. J. Chem. Inf. Model. 60 (4) (2020)
Li Fu, Lu Liu, Zhi-Jiang Yang, Pan Li, Jun-Jie Ding, Yong-Huan Yun, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis. J. Chem. Inf. Model. 60 (1) (2020)

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Tingjun Hou