Tingjun Hou

197 papers A* 3Journal 193Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
NavDB: A Comprehensive Database for Voltage-Gated Sodium Channels Modulators and Targets.
J. Chem. Inf. Model.
Gaoang Wang, Jiahui Yu, Haiyi Chen, Hao Luo, Peichen Pan, Tingjun Hou
2026 J jnl
SynGFN: learning across chemical space with generative flow-based molecular discovery.
Nat. Comput. Sci.
Yuchen Zhu, Shuwang Li, Jihong Chen, Donghai Zhao, Xiaorui Wang, Yitong Li, Yifei Liu, Yue Kong, Beichen Zhang, Chang Liu, Tingjun Hou, Chang-Yu Hsieh
2026 J jnl
Understanding the Kinetic Mechanism of Ligands Stabilizing the RAS-CYPA Interaction.
J. Chem. Inf. Model.
Kexin Xu, Mingyun Shen, Zhe Wang, Sutong Xiang, Qirui Deng, Kaimo Yang, Zhiliang Jiang, Zihao Wang, Chen Yin, Tingjun Hou, Huiyong Sun
2025 J jnl
A Scalable and Quantum-Accurate Foundation Model for Biomolecular Force Field via Linearly Tensorized Quadrangle Attention.
CoRR
Qun Su, Kai Zhu, Qiaolin Gou, Jintu Zhang, Renling Hu, Yurong Li, Yongze Wang, Hui Zhang, Ziyi You, Linlong Jiang, Yu Kang, Jike Wang, Chang-Yu Hsieh, Tingjun Hou
2025 J jnl
A Unified Deep Graph Model for Identifying the Molecular Categories of Ligands Targeting Nuclear Receptors.
J. Chem. Inf. Model.
Kaimo Yang, Dejun Jiang, Qirui Deng, Sutong Xiang, Jingxuan Ge, Kexin Xu, Zhiliang Jiang, Zihao Wang, Chen Yin, Youqiao Qian, Tingjun Hou, Huiyong Sun
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
Allosteric Cooperativity Mechanism Investigation of Orthosteric and Allosteric Ligands in Modulating AR Activity: A Molecular Dynamics Study.
J. Chem. Inf. Model.
Xiaotian Kong, Yushan Zou, Peng Cao, Yuxuan Dong, Keran Li, Xi Zhang, Yubo Liu, Sijin Wu, Sheng Tian, Chunhua Li, Tingjun Hou
2025 J jnl
Benchmarking AI-powered docking methods from the perspective of virtual screening.
Nat. Mac. Intell.
Shukai Gu, Chao Shen, Xujun Zhang, Huiyong Sun, Heng Cai, Hao Luo, Huifeng Zhao, Bo Liu, Hongyan Du, Yihao Zhao, Chenggong Fu, Silong Zhai, Yafeng Deng, Huanxiang Liu, Tingjun Hou, Yu Kang
2025 J jnl
BioScore: A Foundational Scoring Function For Diverse Biomolecular Complexes.
CoRR
Yuchen Zhu, Jihong Chen, Yitong Li, Xiaomin Fang, Xianbin Ye, Jingzhou He, Xujun Zhang, Jingxuan Ge, Chao Shen, Xiaonan Zhang, Tingjun Hou, Chang-Yu Hsieh
2025 J jnl
ChargeNet: E(3) Equivariant Graph Attention Network for Atomic Charge Prediction.
J. Chem. Inf. Model.
Qiaolin Gou, Qun Su, Jike Wang, Hui Zhang, Huiyong Sun, Xujun Zhang, Linlong Jiang, Meijing Fang, Yu Kang, Huanxiang Liu, Tingjun Hou, Chang-Yu Hsieh
2025 J jnl
Comprehensive Evaluation of End-Point Free Energy Methods in DNA-Ligand Interaction Predictions.
J. Chem. Inf. Model.
Cuiyu Li, Hongyan Du, Chengwei Zhang, Wanying Huang, Xujun Zhang, Tianyue Wang, Dejun Jiang, Tingjun Hou, Ercheng Wang
2025 J jnl
Deep Learning-Driven Insights into Enzyme-Substrate Interaction Discovery.
J. Chem. Inf. Model.
Wenjia Qian, Xiaorui Wang, Yuansheng Huang, Yu Kang, Peichen Pan, Chang-Yu Hsieh, 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
2025 J jnl
ECloudGen: leveraging electron clouds as a latent variable to scale up structure-based molecular design.
Nat. Comput. Sci.
Odin Zhang, Jieyu Jin, Zhenxing Wu, Jintu Zhang, Po Yuan, Yuntao Yu, Haitao Lin, Haiyang Zhong, Xujun Zhang, Chenqing Hua, Weibo Zhao, Zhengshuo Zhang, Kejun Ying, Yufei Huang, Huifeng Zhao, Yu Kang, Peichen Pan, Jike Wang, Dong Guo, Shuangjia Zheng, Chang-Yu Hsieh, Tingjun Hou
2025 J jnl
Graph Neural Networks in Modern AI-aided Drug Discovery.
CoRR
Odin Zhang, Haitao Lin, Xujun Zhang, Xiaorui Wang, Zhenxing Wu, Qing Ye, Weibo Zhao, Jike Wang, Kejun Ying, Yu Kang, Chang-Yu Hsieh, Tingjun Hou
2025 J jnl
Improving the predictive performance of binding affinities and poses for protein-cyclic peptide complexes through fine-tuned MM/PBSA(GBSA)-based methods.
Briefings Bioinform.
Huifeng Zhao, Jianxiang Huang, Gaoqi Weng, Dejun Jiang, Renling Hu, Yu Kang, Tingjun Hou
2025 J jnl
PepBAN: A Deep Learning Framework with Bilinear Attention and Adversarial Learning for Peptide-Protein Interaction Prediction.
J. Chem. Inf. Model.
Shuaiyan Li, Xiaorui Wang, Yuchen Zhu, Jingxuan Ge, Donghai Zhao, Hongxia Xu, Tingjun Hou, Chang-Yu Hsieh
2025 J jnl
PepPCBench is a Comprehensive Benchmarking Framework for Protein-Peptide Complex Structure Prediction.
J. Chem. Inf. Model.
Silong Zhai, Huifeng Zhao, Jike Wang, Shaolong Lin, Tiantao Liu, Shukai Gu, Dejun Jiang, Huanxiang Liu, Yu Kang, Xiaojun Yao, Tingjun Hou
2025 J jnl
ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings.
CoRR
Zitai Kong, Yiheng Zhu, Yinlong Xu, Hanjing Zhou, Mingzhe Yin, Jialu Wu, Hongxia Xu, Chang-Yu Hsieh, Tingjun Hou, Jian Wu
2025 J jnl
Revisiting Protein-Protein Docking: A Systematic Evaluation Framework.
J. Chem. Inf. Model.
Linlong Jiang, Ke Zhang, Kai Zhu, Ying Wang, Yu Kang, Tingjun Hou
2025 J jnl
Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates.
J. Cheminformatics
Xiaodan Yin, Xiaorui Wang, Zhenxing Wu, Qin Li, Yu Kang, Yafeng Deng, Pei Luo, Huanxiang Liu, Guqin Shi, Zheng Wang, Xiaojun Yao, Chang-Yu Hsieh, Tingjun Hou
2025 A* conf
Synergy of GFlowNet and Protein Language Model Makes a Diverse Antibody Designer.
AAAI
Mingze Yin, Hanjing Zhou, Yiheng Zhu, Jialu Wu, Wei Wu, Mingyang Li, Kun Fu, Zheng Wang, Chang-Yu Hsieh, Tingjun Hou, Jian Wu
2025 J jnl
Toward Closed-loop Molecular Discovery via Language Model, Property Alignment and Strategic Search.
CoRR
Junkai Ji, Zhangfan Yang, Dong Xu, Ruibin Bai, Jian-Qiang Li, Tingjun Hou, Zexuan Zhu
2024 J jnl
A general model for predicting enzyme functions based on enzymatic reactions.
J. Cheminformatics
Wenjia Qian, Xiaorui Wang, Yu Kang, Peichen Pan, Tingjun Hou, Chang-Yu Hsieh
2024 J jnl
AAVDiff: Experimental Validation of Enhanced Viability and Diversity in Recombinant Adeno-Associated Virus (AAV) Capsids through Diffusion Generation.
CoRR
Lijun Liu, Jiali Yang, Jianfei Song, Xinglin Yang, Lele Niu, Zeqi Cai, Hui Shi, Tingjun Hou, Chang-Yu Hsieh, Weiran Shen, Yafeng Deng
2024 J jnl
AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences.
Briefings Bioinform.
Ruofan Jin, Qing Ye, Jike Wang, Zheng Cao, Dejun Jiang, Tianyue Wang, Yu Kang, Wanting Xu, Chang-Yu Hsieh, Tingjun Hou
2024 J jnl
Characterizing the Cooperative Effect of PROTAC Systems with End-Point Binding Free Energy Calculation.
J. Chem. Inf. Model.
Kexin Xu, Zhe Wang, Sutong Xiang, Rongfan Tang, Qirui Deng, Jingxuan Ge, Zhiliang Jiang, Kaimo Yang, Tingjun Hou, Huiyong Sun
2024 J jnl
Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes.
J. Chem. Inf. Model.
Huifeng Zhao, Dejun Jiang, Chao Shen, Jintu Zhang, Xujun Zhang, Xiaorui Wang, Dou Nie, Tingjun Hou, Yu Kang
2024 J jnl
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.
Briefings Bioinform.
Tianyue Wang, Langcheng Wang, Xujun Zhang, Chao Shen, Odin Zhang, Jike Wang, Jialu Wu, Ruofan Jin, Donghao Zhou, Shicheng Chen, Liwei Liu, Xiaorui Wang, Chang-Yu Hsieh, Guangyong Chen, Peichen Pan, Yu Kang, Tingjun Hou
2024 J jnl
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation.
CoRR
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
2024 J jnl
Deep Lead Optimization: Leveraging Generative AI for Structural Modification.
CoRR
Odin Zhang, Haitao Lin, Hui Zhang, Huifeng Zhao, Yufei Huang, Yuansheng Huang, Dejun Jiang, Chang-Yu Hsieh, Peichen Pan, Tingjun Hou
2024 J jnl
Discovery of Potent Covalent CRM1 Inhibitors Via a Customized Structure-Based Virtual Screening Pipeline and Bioassays.
J. Chem. Inf. Model.
He Liu, Chao Shen, Haonan Li, Tingjun Hou, Yongliang Yang
2024 J jnl
Dissecting the role of ALK double mutations in drug resistance to lorlatinib with in-depth theoretical modeling and analysis.
Comput. Biol. Medicine
Xing Zhang, Jianbo Tong, Tianhao Wang, Tianyue Wang, Lei Xu, Zhe Wang, Tingjun Hou, Peichen Pan
2024 J jnl
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery.
J. Chem. Inf. Model.
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
2024 J jnl
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios.
J. Chem. Inf. Model.
Shukai Gu, Yuwei Yang, Yihao Zhao, Jiayue Qiu, Xiaorui Wang, Henry Hoi Yee Tong, Liwei Liu, Xiaozhe Wan, Huanxiang Liu, Tingjun Hou, Yu Kang
2024 J jnl
Generative AI for Controllable Protein Sequence Design: A Survey.
CoRR
Yiheng Zhu, Zitai Kong, Jialu Wu, Weize Liu, Yuqiang Han, Mingze Yin, Hongxia Xu, Chang-Yu Hsieh, Tingjun Hou
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
2024 J jnl
In-depth theoretical modeling to explore the mechanism of TPX-0131 overcoming lorlatinib resistance to ALKL1196M/G1202R mutation.
Comput. Biol. Medicine
Xing Zhang, Jianbo Tong, Tianhao Wang, Zhe Wang, Shukai Gu, Lei Xu, Tingjun Hou, Peichen Pan
2024 J jnl
Leveraging language model for advanced multiproperty molecular optimization via prompt engineering.
Nat. Mac. Intell.
Zhenxing Wu, Odin Zhang, Xiaorui Wang, Li Fu, Huifeng Zhao, Jike Wang, Hongyan Du, Dejun Jiang, Yafeng Deng, Dong-Sheng Cao, Chang-Yu Hsieh, Tingjun Hou
2024 J jnl
Multi-Modal CLIP-Informed Protein Editing.
CoRR
Mingze Yin, Hanjing Zhou, Yiheng Zhu, Miao Lin, Yixuan Wu, Jialu Wu, Hongxia Xu, Chang-Yu Hsieh, Tingjun Hou, Jintai Chen, Jian Wu
2024 J jnl
Multiscale topology in interactomic network: from transcriptome to antiaddiction drug repurposing.
Briefings Bioinform.
Hongyan Du, Guo-Wei Wei, Tingjun Hou
2024 J jnl
RLpMIEC: High-Affinity Peptide Generation Targeting Major Histocompatibility Complex-I Guided and Interpreted by Interaction Spectrum-Navigated Reinforcement Learning.
J. Chem. Inf. Model.
Qirui Deng, Zhe Wang, Sutong Xiang, Qinghua Wang, Yifei Liu, Tingjun Hou, Huiyong Sun
2024 J jnl
S
CoRR
Mingze Yin, Hanjing Zhou, Jialu Wu, Yiheng Zhu, Yuxuan Zhan, Zitai Kong, Hongxia Xu, Chang-Yu Hsieh, Jintai Chen, Tingjun Hou, Jian Wu
2024 J jnl
Structure-based virtual screening of novel USP5 inhibitors targeting the zinc finger ubiquitin-binding domain.
Comput. Biol. Medicine
Tianhao Wang, Jianbo Tong, Xing Zhang, Zhe Wang, Lei Xu, Peichen Pan, Tingjun Hou
2024 J jnl
Token-Mol 1.0: Tokenized drug design with large language model.
CoRR
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
2024 J jnl
TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides.
J. Chem. Inf. Model.
Nanqi Hong, Dejun Jiang, Zhe Wang, Huiyong Sun, Hao Luo, Lingjie Bao, Mingli Song, Yu Kang, Tingjun Hou
2023 J jnl
CODD-Pred: A Web Server for Efficient Target Identification and Bioactivity Prediction of Small Molecules.
J. Chem. Inf. Model.
Xiaodan Yin, Xiaorui Wang, Yuquan Li, Jike Wang, Yuwei Wang, Yafeng Deng, Tingjun Hou, Huanxiang Liu, Pei Luo, Xiaojun Yao
2023 J jnl
Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning?
Briefings Bioinform.
Shukai Gu, Chao Shen, Jiahui Yu, Hong Zhao, Huanxiang Liu, Liwei Liu, Rong Sheng, Lei Xu, Zhe Wang, Tingjun Hou, Yu Kang
2023 J jnl
Comprehensive assessment of nine target prediction web services: which should we choose for target fishing?
Briefings Bioinform.
Kai-Yue Ji, Chong Liu, Zhao-Qian Liu, Yafeng Deng, Tingjun Hou, Dong-Sheng Cao
2023 J jnl
Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis.
Briefings Bioinform.
Lingling Wang, Lei Xu, Zhe Wang, Tingjun Hou, Haiping Hao, Huiyong Sun
2023 J jnl
CovInter: interaction data between coronavirus RNAs and host proteins.
Nucleic Acids Res.
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
2023 J jnl
Deep Generation Model Guided by the Docking Score for Active Molecular Design.
J. Chem. Inf. Model.
Yuwei Yang, Chang-Yu Hsieh, Yu Kang, Tingjun Hou, Huanxiang Liu, Xiaojun Yao
2023 J jnl
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.
Yuchen Sun, Xibing He, Tingjun Hou, Lianjin Cai, Viet Hoang Man, Junmei Wang
2023 J jnl
Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of
J. Comput. Chem.
Yuchen Sun, Tingjun Hou, Xibing He, Viet Hoang Man, Junmei Wang
2023 J jnl
DrugMAP: molecular atlas and pharma-information of all drugs.
Nucleic Acids Res.
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
2023 J jnl
Efficient and accurate large library ligand docking with KarmaDock.
Nat. Comput. Sci.
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
2023 J jnl
Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor
J. Chem. Inf. Model.
Sutong Xiang, Zhe Wang, Rongfan Tang, Lingling Wang, Qinghua Wang, Yang Yu, Qirui Deng, Tingjun Hou, Haiping Hao, Huiyong Sun
2023 J jnl
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery.
J. Chem. Inf. Model.
Zhenxing Wu, Jihong Chen, Yitong Li, Yafeng Deng, Haitao Zhao, Chang-Yu Hsieh, Tingjun Hou
2023 J jnl
From molecules to scaffolds to functional groups: building context-dependent molecular representation via multi-channel learning.
CoRR
Yue Wan, Jialu Wu, Tingjun Hou, Chang-Yu Hsieh, Xiaowei Jia
2023 J jnl
Improved GNNs for Log 
J. Chem. Inf. Model.
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
2023 J jnl
In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences.
J. Cheminformatics
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
2023 J jnl
Learning on topological surface and geometric structure for 3D molecular generation.
Nat. Comput. Sci.
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
2023 J jnl
Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors.
Briefings Bioinform.
Dong Wang, Zhenxing Wu, Chao Shen, Lingjie Bao, Hao Luo, Zhe Wang, Hucheng Yao, De-Xin Kong, Cheng Luo, 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
MetaRF: attention-based random forest for reaction yield prediction with a few trails.
J. Cheminformatics
Kexin Chen, Guangyong Chen, Junyou Li, Yuansheng Huang, Ercheng Wang, Tingjun Hou, Pheng-Ann Heng
2023 A* conf
MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation.
IJCAI
Yiheng Zhu, Zhenqiu Ouyang, Ben Liao, Jialu Wu, Yixuan Wu, Chang-Yu Hsieh, Tingjun Hou, Jian Wu
2023 J jnl
MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation.
CoRR
Yiheng Zhu, Zhenqiu Ouyang, Ben Liao, Jialu Wu, Yixuan Wu, Chang-Yu Hsieh, Tingjun Hou, Jian Wu
2023 J jnl
Molecular Generation with Reduced Labeling through Constraint Architecture.
J. Chem. Inf. Model.
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
2023 J jnl
Multiscale Topology in Interactomic Network: From Transcriptome to Antiaddiction Drug Repurposing.
CoRR
Hongyan Du, Guo-Wei Wei, Tingjun Hou
2023 J jnl
On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate.
J. Chem. Inf. Model.
Haiyi Chen, Yue Guo, Shengqing Ye, Jintu Zhang, Haotian Zhang, Na Liu, Rui Zhou, Tingjun Hou, Hongguang Xia, Yu Kang, Mojie Duan
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
2023 J jnl
Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials.
J. Chem. Inf. Model.
Jintu Zhang, Haotian Zhang, ZhiXin Qin, Yu Kang, Xin Hong, Tingjun Hou
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
2023 J jnl
Recent advances in artificial intelligence for retrosynthesis.
CoRR
Zipeng Zhong, Jie Song, Zunlei Feng, Tiantao Liu, Lingxiang Jia, Shaolun Yao, Tingjun Hou, Mingli Song
2023 J jnl
Reducing false positive rate of docking-based virtual screening by active learning.
Briefings Bioinform.
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
2023 J jnl
ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling.
Nat. Mac. Intell.
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
2023 A* conf
Sample-efficient Multi-objective Molecular Optimization with GFlowNets.
NeurIPS
Yiheng Zhu, Jialu Wu, Chaowen Hu, Jiahuan Yan, Chang-Yu Hsieh, Tingjun Hou, Jian Wu
2023 J jnl
Sample-efficient Multi-objective Molecular Optimization with GFlowNets.
CoRR
Yiheng Zhu, Jialu Wu, Chaowen Hu, Jiahuan Yan, Chang-Yu Hsieh, Tingjun Hou, Jian Wu
2023 J jnl
Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets.
J. Chem. Inf. Model.
Zhe Wang, Haiyang Zhong, Jintu Zhang, Peichen Pan, Dong Wang, Huanxiang Liu, Xiaojun Yao, Tingjun Hou, Yu Kang
2023 J jnl
Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches.
J. Chem. Inf. Model.
Teng-Zhi Long, Shao-Hua Shi, Shao Liu, Ai-Ping Lu, Zhao-Qian Liu, Min Li, Tingjun Hou, Dong-Sheng Cao
2023 J jnl
TB-IECS: an accurate machine learning-based scoring function for virtual screening.
J. Cheminformatics
Xujun Zhang, Chao Shen, Dejun Jiang, Jintu Zhang, Qing Ye, Lei Xu, Tingjun Hou, Peichen Pan, Yu Kang
2023 J jnl
TransFoxMol: predicting molecular property with focused attention.
Briefings Bioinform.
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
2022 J jnl
ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images.
Briefings Bioinform.
Xiao-Chen Zhang, Jiacai Yi, Guo-Ping Yang, Chengkun Wu, Tingjun Hou, Dong-Sheng Cao
2022 J jnl
ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction.
J. Chem. Inf. Model.
Jialu Wu, Junmei Wang, Zhenxing Wu, Shengyu Zhang, Yafeng Deng, Yu Kang, Dong-Sheng Cao, Chang-Yu Hsieh, Tingjun Hou
2022 J jnl
Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations.
Briefings Bioinform.
Rongfan Tang, Pengcheng Chen, Zhe Wang, Lingling Wang, Haiping Hao, Tingjun Hou, Huiyong Sun
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
DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety.
Nucleic Acids Res.
Guo-Li Xiong, Zhi-Jiang Yang, Jiacai Yi, Ningning Wang, Lei Wang, Huimin Zhu, Chengkun Wu, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dongsheng Cao
2022 J jnl
Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning.
J. Chem. Inf. Model.
Qinghua Wang, Zhe Wang, Sheng Tian, Lingling Wang, Rongfan Tang, Yang Yu, Jingxuan Ge, Tingjun Hou, Haiping Hao, Huiyong Sun
2022 J jnl
Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation.
J. Chem. Inf. Model.
Yuwei Yang, Zhenxing Wu, Xiaojun Yao, Yu Kang, Tingjun Hou, Chang-Yu Hsieh, Huanxiang Liu
2022 J jnl
Knowledge-based BERT: a method to extract molecular features like computational chemists.
Briefings Bioinform.
Zhenxing Wu, Dejun Jiang, Jike Wang, Xujun Zhang, Hongyan Du, Lurong Pan, Chang-Yu Hsieh, Dongsheng Cao, Tingjun Hou
2022 J jnl
MICER: a pre-trained encoder-decoder architecture for molecular image captioning.
Bioinform.
Jiacai Yi, Chengkun Wu, Xiao-Chen Zhang, Xinyi Xiao, Yanlong Qiu, Wentao Zhao, Tingjun Hou, Dong-Sheng Cao
2022 J jnl
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes.
J. Cheminformatics
Ning-Ning Wang, Xiang-Gui Wang, Guo-Li Xiong, Ziyi Yang, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dong-Sheng Cao
2022 J jnl
Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands.
J. Chem. Inf. Model.
Haiyi Chen, Rui Zhou, Jinping Pang, Yue Guo, Jiawen Chen, Yu Kang, Mojie Duan, Tingjun Hou
2022 J jnl
Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism.
J. Chem. Inf. Model.
Jiahui Yu, Jike Wang, Hong Zhao, Junbo Gao, Yu Kang, Dong-Sheng Cao, Zhe Wang, Tingjun Hou
2022 J jnl
Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning.
Briefings Bioinform.
Dejun Jiang, Huiyong Sun, Jike Wang, Chang-Yu Hsieh, Yuquan Li, Zhenxing Wu, Dong-Sheng Cao, Jian Wu, Tingjun Hou
2022 J jnl
Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses.
J. Cheminformatics
Yang Yu, Zhe Wang, Lingling Wang, Sheng Tian, Tingjun Hou, Huiyong Sun
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
Root-aligned SMILES for Molecular Retrosynthesis Prediction.
CoRR
Zipeng Zhong, Jie Song, Zunlei Feng, Tiantao Liu, Lingxiang Jia, Shaolun Yao, Min Wu, Tingjun Hou, Mingli Song
2022 J jnl
VGSC-DB: an online database of voltage-gated sodium channels.
J. Cheminformatics
Gaoang Wang, Jiahui Yu, Hongyan Du, Chao Shen, Xujun Zhang, Yifei Liu, Yangyang Zhang, Dong-Sheng Cao, Peichen Pan, Tingjun Hou
2022 J jnl
fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation.
Briefings Bioinform.
Zhe Wang, Hong Pan, Huiyong Sun, Yu Kang, Huanxiang Liu, Dongsheng Cao, Tingjun Hou
2021 J jnl
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties.
Nucleic Acids Res.
Guo-Li Xiong, Zhenxing Wu, Jiacai Yi, Li Fu, Zhi-Jiang Yang, Chang-Yu Hsieh, Mingzhu Yin, Xiangxiang Zeng, Chengkun Wu, Aiping Lu, Xiang Chen, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions.
J. Cheminformatics
Xujun Zhang, Chao Shen, Xueying Guo, Zhe Wang, Gaoqi Weng, Qing Ye, Gaoang Wang, Qiaojun He, Bo Yang, Dong-Sheng Cao, 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
Beware of the generic machine learning-based scoring functions in structure-based virtual screening.
Briefings Bioinform.
Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Jinping Pang, Gaoang Wang, Haiyang Zhong, Lei Xu, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study.
Briefings Bioinform.
Jie Dong, Min-Feng Zhu, Yong-Huan Yun, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions.
Briefings Bioinform.
Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Haiyang Zhong, Gaoang Wang, Xiaojun Yao, Lei Xu, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds.
Briefings Bioinform.
Ziyi Yang, Jie Dong, Zhi-Jiang Yang, Mingzhu Yin, Hong-Li Jiang, Ai-Ping Lu, Xiang Chen, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models.
J. Cheminformatics
Dejun Jiang, Zhenxing Wu, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Zhe Wang, Chao Shen, Dong-Sheng Cao, Jian Wu, 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
DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges.
Briefings Bioinform.
Jike Wang, Dong-Sheng Cao, Cunchen Tang, Lei Xu, Qiaojun He, Bo Yang, Xi Chen, Huiyong Sun, Tingjun Hou
2021 J jnl
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.
Zhenxing Wu, Minfeng Zhu, Yu Kang, Elaine Lai-Han Leung, Tailong Lei, Chao Shen, Dejun Jiang, Zhe Wang, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method.
Briefings Bioinform.
Zhenxing Wu, Dejun Jiang, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, 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
Improving structure-based virtual screening performance via learning from scoring function components.
Briefings Bioinform.
Guo-Li Xiong, Wenling Ye, Chao Shen, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules.
Briefings Bioinform.
Chengkun Wu, Xiao-Chen Zhang, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction.
Briefings Bioinform.
Xiao-Chen Zhang, Chengkun Wu, Zhi-Jiang Yang, Zhen-Xing Wu, Jiacai Yi, Chang-Yu Hsieh, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
Multi-constraint molecular generation based on conditional transformer, knowledge distillation and reinforcement learning.
Nat. Mach. Intell.
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
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
2021 J jnl
PySmash: Python package and individual executable program for representative substructure generation and application.
Briefings Bioinform.
Ziyi Yang, Zhi-Jiang Yang, Yue Zhao, Mingzhu Yin, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
QSAR-assisted-MMPA to expand chemical transformation space for lead optimization.
Briefings Bioinform.
Li Fu, Ziyi Yang, Zhi-Jiang Yang, Mingzhu Yin, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
Scopy: an integrated negative design python library for desirable HTS/VS database design.
Briefings Bioinform.
Ziyi Yang, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion.
J. Cheminformatics
Ziyi Yang, Li Fu, Ai-Ping Lu, Shao Liu, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction.
J. Cheminformatics
Chao Shen, Xueping Hu, Junbo Gao, Xujun Zhang, Haiyang Zhong, Zhe Wang, Lei Xu, Yu Kang, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations.
J. Chem. Inf. Model.
Ercheng Wang, Weitao Fu, Dejun Jiang, Huiyong Sun, Junmei Wang, Xujun Zhang, Gaoqi Weng, Hui Liu, Peng Tao, Tingjun Hou
2020 J jnl
ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning.
J. Cheminformatics
Dejun Jiang, Tailong Lei, Zhe Wang, Chao Shen, Dong-Sheng Cao, 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
2020 J jnl
Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities.
J. Chem. Inf. Model.
Ercheng Wang, Hui Liu, Junmei Wang, Gaoqi Weng, Huiyong Sun, Zhe Wang, Yu Kang, Tingjun Hou
2020 J jnl
Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning.
Bioinform.
Jike Wang, Dong-Sheng Cao, Cunchen Tang, Xi Chen, Huiyong Sun, Tingjun Hou
2020 J jnl
Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring.
J. Chem. Inf. Model.
Wenling Ye, Chao Shen, Guo-Li Xiong, Jun-Jie Ding, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
2020 J jnl
Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays.
J. Chem. Inf. Model.
Ziyi Yang, Jie Dong, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
2020 J jnl
Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis.
J. Chem. Inf. Model.
Li Fu, Lu Liu, Zhi-Jiang Yang, Pan Li, Jun-Jie Ding, Yong-Huan Yun, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
2019 J jnl
ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches.
J. Chem. Inf. Model.
Zhenxing Wu, Tailong Lei, Chao Shen, Zhe Wang, Dong-Sheng Cao, 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
Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery.
J. Chem. Inf. Model.
Ziyi Yang, Zhi-Jiang Yang, Jie Dong, Liang-Liang Wang, Liu-Xia Zhang, Jun-Jie Ding, Xiao-Qin Ding, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
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
Discovery of Novel and Selective Adenosine A
J. Chem. Inf. Model.
Sheng Tian, Xu Wang, Linlang Li, Xiaohu Zhang, Youyong Li, Feng Zhu, Tingjun Hou, Xuechu Zhen
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
2016 J jnl
CaFE: a tool for binding affinity prediction using end-point free energy methods.
Bioinform.
Hui Liu, 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
2015 J jnl
Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease.
J. Chem. Inf. Model.
Nan Li, Richard I. Ainsworth, Bo Ding, Tingjun Hou, Wei Wang
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
2014 J jnl
MORT: a powerful foundational library for computational biology and CADD.
J. Cheminformatics
Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang, Jian Zhang, Tingjun Hou
2014 J jnl
P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape.
PLoS Comput. Biol.
Huiyong Sun, Youyong Li, Sheng Tian, Junmei Wang, Tingjun Hou
2013 — conf
A GPU based Conformational Entropy Calculation Method.
IWBBIO
Qian Zhang, José M. García, Junmei Wang, Tingjun Hou, Horacio Emilio Pérez Sánchez
2013 J jnl
Accelerated Conformational Entropy Calculations Using Graphic Processing Units.
J. Chem. Inf. Model.
Qian Zhang, Junmei Wang, Ginés D. Guerrero, José M. Cecilia, José M. García, Youyong Li, Horacio Emilio Pérez Sánchez, Tingjun Hou
2013 J jnl
Allosite: a method for predicting allosteric sites.
Bioinform.
Wenkang Huang, Shaoyong Lu, Zhimin Huang, Xinyi Liu, Linkai Mou, Yu Luo, Yanlong Zhao, Yaqin Liu, Zhongjie Chen, Tingjun Hou, Jian Zhang
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
Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines.
J. Cheminformatics
Sheng Tian, Youyong Li, Junmei Wang, Xiaojie Xu, Lei Xu, Xiaohong Wang, Lei Chen, Tingjun Hou
2013 J jnl
Feasibility of Using Molecular Docking-Based Virtual Screening for Searching Dual Target Kinase Inhibitors.
J. Chem. Inf. Model.
Shunye Zhou, Youyong 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
2013 J jnl
Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches.
J. Chem. Inf. Model.
Peichen Pan, Youyong Li, Huidong Yu, Huiyong Sun, Tingjun Hou
2013 J jnl
Unraveling the Allosteric Inhibition Mechanism of PTP1B by Free Energy Calculation Based on Umbrella Sampling.
J. Chem. Inf. Model.
Wei Cui, Yuanhua Cheng, Lingling Geng, Den-Sheng Liang, Tingjun Hou, Mingjuan Ji
2012 J jnl
A rule-based algorithm for automatic bond type perception.
J. Cheminformatics
Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang, Liling Zhang, Tingjun Hou
2012 J jnl
ADMET Evaluation in Drug Discovery. 11. PharmacoKinetics Knowledge Base (PKKB): A Comprehensive Database of Pharmacokinetic and Toxic Properties for Drugs.
J. Chem. Inf. Model.
Dongyue Cao, Junmei Wang, Rui Zhou, Youyong Li, Huidong Yu, Tingjun Hou
2012 J jnl
Concerted Movement in pH-Dependent Gating of FocA from Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Zhiwei Feng, Tingjun Hou, Youyong Li
2012 J jnl
Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations.
J. Chem. Inf. Model.
Junmei Wang, Tingjun Hou
2012 J jnl
Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines.
J. Cheminformatics
Mingyun Shen, Sheng Tian, Youyong Li, Qian Li, Xiaojie Xu, Junmei Wang, Tingjun Hou
2012 J jnl
Studies on the Interactions between β
J. Chem. Inf. Model.
Zhiwei Feng, Tingjun Hou, Youyong Li
2012 J jnl
Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase.
J. Chem. Inf. Model.
Lin Li, Youyong Li, Liling Zhang, Tingjun Hou
2011 J jnl
Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient.
J. Comput. Chem.
Junmei Wang, Tingjun Hou
2011 J jnl
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang
2011 J jnl
Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking.
J. Comput. Chem.
Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang
2011 J jnl
Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy.
Bioinform.
Tingjun Hou, Youyong Li, Wei Wang
2010 J jnl
Computational Modeling Toward Understanding Agonist Binding on Dopamine 3.
J. Chem. Inf. Model.
Yaxue Zhao, Xuefeng Lu, Chao-Yie Yang, Zhimin Huang, Wei Fu, Tingjun Hou, Jian Zhang
2010 J jnl
Drug and Drug Candidate Building Block Analysis.
J. Chem. Inf. Model.
Junmei Wang, Tingjun Hou
2010 J jnl
Structure-Based Design of Peptides against G3BP with Cytotoxicity on Tumor Cells.
J. Chem. Inf. Model.
Wei Cui, Zhuo Wei, Quan Chen, Yuanhua Cheng, Lingling Geng, Jian Zhang, Jianhua Chen, Tingjun Hou, Mingjuan Ji
2009 J jnl
Aqueous Solubility Prediction Based on Weighted Atom Type Counts and Solvent Accessible Surface Areas.
J. Chem. Inf. Model.
Junmei Wang, Tingjun Hou, Xiaojie Xu
2007 J jnl
ADME Evaluation in Drug Discovery, 6. Can Oral Bioavailability in Humans Be Effectively Predicted by Simple Molecular Property-Based Rules?
J. Chem. Inf. Model.
Tingjun Hou, Junmei Wang, Wei Zhang, Xiaojie Xu
2007 J jnl
ADME Evaluation in Drug Discovery, 7. Prediction of Oral Absorption by Correlation and Classification.
J. Chem. Inf. Model.
Tingjun Hou, Junmei Wang, Wei Zhang, Xiaojie Xu
2007 J jnl
ADME Evaluation in Drug Discovery, 8. The Prediction of Human Intestinal Absorption by a Support Vector Machine.
J. Chem. Inf. Model.
Tingjun Hou, Junmei Wang, Youyong Li
2007 J jnl
Development of Reliable Aqueous Solubility Models and Their Application in Druglike Analysis.
J. Chem. Inf. Model.
Junmei Wang, George Krudy, Tingjun Hou, Wei Zhang, George Holland, Xiaojie Xu
2007 J jnl
On the detection of functionally coherent groups of protein domains with an extension to protein annotation.
BMC Bioinform.
William A. McLaughlin, Ken Chen, Tingjun Hou, Wei Wang
2006 J jnl
Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain.
PLoS Comput. Biol.
Tingjun Hou, Ken Chen, William A. McLaughlin, Benzhuo Lu, Wei Wang
2005 J jnl
New Born Radii Deriving Method for Generalized Born Model.
J. Chem. Inf. Model.
Wei Zhang, Tingjun Hou, Xiaojie Xu
2004 J jnl
ADME Evaluation in Drug Discovery. 2. Prediction of Partition Coefficient by Atom-Additive Approach Based on Atom-Weighted Solvent Accessible Surface Areas [J. Chem. Inf. Comput. Sci. 1058-1067(2003)].
J. Chem. Inf. Model.
Tingjun Hou, Xiaojie Xu
2004 J jnl
ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors [J. Chem. Inf. Comput. Sci. 43, 2137-2152 (2003)]
J. Chem. Inf. Model.
Tingjun Hou, Xiaojie Xu
2004 J jnl
ADME Evaluation in Drug Discovery. 4. Prediction of Aqueous Solubility Based on Atom Contribution Approach.
J. Chem. Inf. Model.
Tingjun Hou, Ke Xia, Wei Zhang, Xiaojie Xu
2004 J jnl
ADME Evaluation in Drug Discovery. 5. Correlation of Caco-2 Permeation with Simple Molecular Properties.
J. Chem. Inf. Model.
Tingjun Hou, Wei Zhang, Ke Xia, Xuebin Qiao, Xiaojie Xu
2004 J jnl
Some Basic Data Structures and Algorithms for Chemical Generic Programming.
J. Chem. Inf. Model.
Wei Zhang, Tingjun Hou, Xuebin Qiao, Xiaojie Xu
2003 J jnl
ADME Evaluation in Drug Discovery. 2. Prediction of Partition Coefficient by Atom-Additive Approach Based on Atom-Weighted Solvent Accessible Surface Areas.
J. Chem. Inf. Comput. Sci.
Tingjun Hou, Xiaojie Xu
2003 J jnl
ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors.
J. Chem. Inf. Comput. Sci.
Tingjun Hou, Xiaojie Xu
2003 J jnl
Mapping the Binding Site of a Large Set of Quinazoline Type EGF-R Inhibitors Using Molecular Field Analyses and Molecular Docking Studies.
J. Chem. Inf. Comput. Sci.
Tingjun Hou, Lili Zhu, Lirong Chen, Xiaojie Xu
2002 J jnl
A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs.
J. Chem. Inf. Comput. Sci.
Xuebin Qiao, Tingjun Hou, Wei Zhang, SenLi Guo, Xiaojie Xu
2002 J jnl
Molecular docking studies of a group of hydroxamate inhibitors with gelatinase-A by molecular dynamics.
J. Comput. Aided Mol. Des.
Tingjun Hou, Wei Zhang, Xiaojie Xu
2001 J jnl
3D QSAR Analyses of Novel Tyrosine Kinase Inhibitors Based on Pharmacophore Alignment.
J. Chem. Inf. Comput. Sci.
Lili Zhu, Tingjun Hou, Lirong Chen, Xiaojie Xu
2000 J jnl
Three-Dimensional Quantitative Structure-Activity Relationship Analysis of the New Potent Sulfonylureas Using Comparative Molecular Similarity Indices Analysis.
J. Chem. Inf. Comput. Sci.
Tingjun Hou, Z. M. Li, Z. Li, J. Liu, Xiaojie Xu
1999 J jnl
Applications of Genetic Algorithms on the Structure-Activity Relationship Analysis of Some Cinnamamides.
J. Chem. Inf. Comput. Sci.
Tingjun Hou, Junmei Wang, N. Liao, Xiaojie Xu