Applications of Genetic Algorithms on the Structure-Activity Relationship Analysis of Some Cinnamamides. - Tingjun Hou; Junmei Wang; N. Liao; Xiaojie Xu (J. Chem. Inf. Comput. Sci., 1999)

Three-Dimensional Quantitative Structure-Activity Relationship Analysis of the New Potent Sulfonylureas Using Comparative Molecular Similarity Indices Analysis. - Tingjun Hou; Z. M. Li; Z. Li; J. Liu; Xiaojie Xu (J. Chem. Inf. Comput. Sci., 2000)

3D QSAR Analyses of Novel Tyrosine Kinase Inhibitors Based on Pharmacophore Alignment. - Lili Zhu; Tingjun Hou; Lirong Chen; Xiaojie Xu (J. Chem. Inf. Comput. Sci., 2001)

Molecular docking studies of a group of hydroxamate inhibitors with gelatinase-A by molecular dynamics. - Tingjun Hou; Wei Zhang 019; Xiaojie Xu (J. Comput. Aided Mol. Des., 2002)

A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs. - Xuebin Qiao; Tingjun Hou; Wei Zhang 019; SenLi Guo; Xiaojie Xu (J. Chem. Inf. Comput. Sci., 2002)

ADME Evaluation in Drug Discovery. 2. Prediction of Partition Coefficient by Atom-Additive Approach Based on Atom-Weighted Solvent Accessible Surface Areas. - Tingjun Hou; Xiaojie Xu (J. Chem. Inf. Comput. Sci., 2003)

ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors. - Tingjun Hou; Xiaojie Xu (J. Chem. Inf. Comput. Sci., 2003)

Mapping the Binding Site of a Large Set of Quinazoline Type EGF-R Inhibitors Using Molecular Field Analyses and Molecular Docking Studies. - Tingjun Hou; Lili Zhu; Lirong Chen; Xiaojie Xu (J. Chem. Inf. Comput. Sci., 2003)

ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors [J. Chem. Inf. Comput. Sci. 43, 2137-2152 (2003)] - Tingjun Hou; Xiaojie Xu (J. Chem. Inf. Model., 2004)

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)]. - Tingjun Hou; Xiaojie Xu (J. Chem. Inf. Model., 2004)

ADME Evaluation in Drug Discovery. 4. Prediction of Aqueous Solubility Based on Atom Contribution Approach. - Tingjun Hou; Ke Xia; Wei Zhang 019; Xiaojie Xu (J. Chem. Inf. Model., 2004)

ADME Evaluation in Drug Discovery. 5. Correlation of Caco-2 Permeation with Simple Molecular Properties. - Tingjun Hou; Wei Zhang 019; Ke Xia; Xuebin Qiao; Xiaojie Xu (J. Chem. Inf. Model., 2004)

Some Basic Data Structures and Algorithms for Chemical Generic Programming. - Wei Zhang 019; Tingjun Hou; Xuebin Qiao; Xiaojie Xu (J. Chem. Inf. Model., 2004)

New Born Radii Deriving Method for Generalized Born Model. - Wei Zhang 019; Tingjun Hou; Xiaojie Xu (J. Chem. Inf. Model., 2005)

Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain. - Tingjun Hou; Ken Chen 001; William A. McLaughlin; Benzhuo Lu; Wei Wang 051 (PLoS Comput. Biol., 2006)

On the detection of functionally coherent groups of protein domains with an extension to protein annotation. - William A. McLaughlin; Ken Chen 001; Tingjun Hou; Wei Wang 051 (BMC Bioinform., 2007)

ADME Evaluation in Drug Discovery, 7. Prediction of Oral Absorption by Correlation and Classification. - Tingjun Hou; Junmei Wang; Wei Zhang 019; Xiaojie Xu (J. Chem. Inf. Model., 2007)

ADME Evaluation in Drug Discovery, 6. Can Oral Bioavailability in Humans Be Effectively Predicted by Simple Molecular Property-Based Rules? - Tingjun Hou; Junmei Wang; Wei Zhang 019; Xiaojie Xu (J. Chem. Inf. Model., 2007)

ADME Evaluation in Drug Discovery, 8. The Prediction of Human Intestinal Absorption by a Support Vector Machine. - Tingjun Hou; Junmei Wang; Youyong Li (J. Chem. Inf. Model., 2007)

Development of Reliable Aqueous Solubility Models and Their Application in Druglike Analysis. - Junmei Wang; George Krudy; Tingjun Hou; Wei Zhang 019; George Holland; Xiaojie Xu (J. Chem. Inf. Model., 2007)

Aqueous Solubility Prediction Based on Weighted Atom Type Counts and Solvent Accessible Surface Areas. - Junmei Wang; Tingjun Hou; Xiaojie Xu (J. Chem. Inf. Model., 2009)

Structure-Based Design of Peptides against G3BP with Cytotoxicity on Tumor Cells. - Wei Cui; Zhuo Wei; Quan Chen; Yuanhua Cheng; Lingling Geng; Jian Zhang 037; Jianhua Chen; Tingjun Hou; Mingjuan Ji (J. Chem. Inf. Model., 2010)

Drug and Drug Candidate Building Block Analysis. - Junmei Wang; Tingjun Hou (J. Chem. Inf. Model., 2010)

Computational Modeling Toward Understanding Agonist Binding on Dopamine 3. - Yaxue Zhao; Xuefeng Lu; Chao-Yie Yang; Zhimin Huang; Wei Fu; Tingjun Hou; Jian Zhang 037 (J. Chem. Inf. Model., 2010)

Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy. - Tingjun Hou; Youyong Li; Wei Wang 051 (Bioinform., 2011)

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. - Tingjun Hou; Junmei Wang; Youyong Li; Wei Wang 051 (J. Comput. Chem., 2011)

Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient. - Junmei Wang; Tingjun Hou (J. Comput. Chem., 2011)

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations. - Tingjun Hou; Junmei Wang; Youyong Li; Wei Wang 051 (J. Chem. Inf. Model., 2011)

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. - Mingyun Shen; Sheng Tian; Youyong Li; Qian Li; Xiaojie Xu; Junmei Wang; Tingjun Hou (J. Cheminformatics, 2012)

A rule-based algorithm for automatic bond type perception. - Qian Zhang 063; Wei Zhang 019; Youyong Li; Junmei Wang; Liling Zhang; Tingjun Hou (J. Cheminformatics, 2012)

ADMET Evaluation in Drug Discovery. 11. PharmacoKinetics Knowledge Base (PKKB): A Comprehensive Database of Pharmacokinetic and Toxic Properties for Drugs. - Dongyue Cao; Junmei Wang; Rui Zhou; Youyong Li; Huidong Yu; Tingjun Hou (J. Chem. Inf. Model., 2012)

Studies on the Interactions between β2 Adrenergic Receptor and Gs Protein by Molecular Dynamics Simulations. - Zhiwei Feng; Tingjun Hou; Youyong Li (J. Chem. Inf. Model., 2012)

Concerted Movement in pH-Dependent Gating of FocA from Molecular Dynamics Simulations. - Zhiwei Feng; Tingjun Hou; Youyong Li (J. Chem. Inf. Model., 2012)

Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase. - Lin Li; Youyong Li; Liling Zhang; Tingjun Hou (J. Chem. Inf. Model., 2012)

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations. - Junmei Wang; Tingjun Hou (J. Chem. Inf. Model., 2012)

A GPU based Conformational Entropy Calculation Method. - Qian Zhang 063; José M. García 001; Junmei Wang; Tingjun Hou; Horacio Emilio Pérez Sánchez (IWBBIO, 2013)

Allosite: a method for predicting allosteric sites. - Wenkang Huang; Shaoyong Lu; Zhimin Huang; Xinyi Liu 003; Linkai Mou; Yu Luo; Yanlong Zhao; Yaqin Liu; Zhongjie Chen; Tingjun Hou; Jian Zhang 037 (Bioinform., 2013)

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. - Sheng Tian; Youyong Li; Junmei Wang; Xiaojie Xu; Lei Xu 035; Xiaohong Wang; Lei Chen; Tingjun Hou (J. Cheminformatics, 2013)

Unraveling the Allosteric Inhibition Mechanism of PTP1B by Free Energy Calculation Based on Umbrella Sampling. - Wei Cui; Yuanhua Cheng; Lingling Geng; Den-Sheng Liang; Tingjun Hou; Mingjuan Ji (J. Chem. Inf. Model., 2013)

Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches. - Peichen Pan; Youyong Li; Huidong Yu; Huiyong Sun; Tingjun Hou (J. Chem. Inf. Model., 2013)

Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches. - Huiyong Sun; Youyong Li; Dan Li 013; Tingjun Hou (J. Chem. Inf. Model., 2013)

Modeling Compound-Target Interaction Network of Traditional Chinese Medicines for Type II Diabetes Mellitus: Insight for Polypharmacology and Drug Design. - Sheng Tian; Youyong Li; Dan Li 013; Xiaojie Xu; Junmei Wang; Qian Zhang 063; Tingjun Hou (J. Chem. Inf. Model., 2013)

Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures. - Sheng Tian; Huiyong Sun; Youyong Li; Peichen Pan; Dan Li 013; Tingjun Hou (J. Chem. Inf. Model., 2013)

Accelerated Conformational Entropy Calculations Using Graphic Processing Units. - Qian Zhang 063; Junmei Wang; Ginés D. Guerrero; José M. Cecilia; José M. García 001; Youyong Li; Horacio Emilio Pérez Sánchez; Tingjun Hou (J. Chem. Inf. Model., 2013)

Feasibility of Using Molecular Docking-Based Virtual Screening for Searching Dual Target Kinase Inhibitors. - Shunye Zhou; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2013)

MORT: a powerful foundational library for computational biology and CADD. - Qian Zhang 063; Wei Zhang 019; Youyong Li; Junmei Wang; Jian Zhang 037; Tingjun Hou (J. Cheminformatics, 2014)

Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility. - Sheng Tian; Huiyong Sun; Peichen Pan; Dan Li 013; Xuechu Zhen; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2014)

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape. - Huiyong Sun; Youyong Li; Sheng Tian; Junmei Wang; Tingjun Hou (PLoS Comput. Biol., 2014)

Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease. - Nan Li; Richard I. Ainsworth; Bo Ding; Tingjun Hou; Wei Wang 051 (J. Chem. Inf. Model., 2015)

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. - Peichen Pan; Sheng Tian; Huiyong Sun; Xiaotian Kong; Wenfang Zhou; Dan Li 013; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2015)

Structure-Activity Relationships and Anti-inflammatory Activities of N-Carbamothioylformamide Analogues as MIF Tautomerase Inhibitors. - Yu Zhang; Lei Xu 035; Zhiqiang Zhang; Zhiyu Zhang; Longtai Zheng; Dan Li 013; Youyong Li; Feng Liu; Kunqian Yu; Tingjun Hou; Xuechu Zhen (J. Chem. Inf. Model., 2015)

CaFE: a tool for binding affinity prediction using end-point free energy methods. - Hui Liu; Tingjun Hou (Bioinform., 2016)

ADMET evaluation in drug discovery: 15. Accurate prediction of rat oral acute toxicity using relevance vector machine and consensus modeling. - Tailong Lei; Youyong Li; Yunlong Song; Dan Li 013; Huiyong Sun; Tingjun Hou (J. Cheminformatics, 2016)

HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. - Ting Feng; Fu Chen; Yu Kang 002; Huiyong Sun; Hui Liu; Dan Li 013; Feng Zhu 004; Tingjun Hou (J. Cheminformatics, 2017)

Comparative analyses of structural features and scaffold diversity for purchasable compound libraries. - Jun Shang; Huiyong Sun; Hui Liu; Fu Chen; Sheng Tian; Peichen Pan; Dan Li 013; De-Xin Kong; Tingjun Hou (J. Cheminformatics, 2017)

Discovery of Novel and Selective Adenosine A2A Receptor Antagonists for Treating Parkinson's Disease through Comparative Structure-Based Virtual Screening. - Sheng Tian; Xu Wang; Linlang Li; Xiaohu Zhang; Youyong Li; Feng Zhu 004; Tingjun Hou; Xuechu Zhen (J. Chem. Inf. Model., 2017)

Characterizing Drug-Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches. - Huiyong Sun; Youyong Li; Mingyun Shen; Dan Li 013; Yu Kang 002; Tingjun Hou (J. Chem. Inf. Model., 2017)

Discovery of Novel Androgen Receptor Ligands by Structure-based Virtual Screening and Bioassays. - Wenfang Zhou; Mojie Duan; Weitao Fu; Jinping Pang; Qin Tang; Huiyong Sun; Lei Xu 035; Shan Chang; Dan Li 013; Tingjun Hou (Genom. Proteom. Bioinform., 2018)

Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator. - Na Liu; Wenfang Zhou; Yue Guo 008; Junmei Wang; Weitao Fu; Huiyong Sun; Dan Li 013; Mojie Duan; Tingjun Hou (J. Chem. Inf. Model., 2018)

Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products. - Jun Shang; Ben Hu; Junmei Wang; Feng Zhu 004; Yu Kang 002; Dan Li 013; Huiyong Sun; De-Xin Kong; Tingjun Hou (J. Chem. Inf. Model., 2018)

farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. - Zhe Wang 041; Xuwen Wang; Youyong Li; Tailong Lei; Ercheng Wang; Dan Li 013; Yu Kang 002; Feng Zhu 004; Tingjun Hou (Bioinform., 2019)

Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations. - Ye Jin; Mojie Duan; Xuwen Wang; Xiaotian Kong; Wenfang Zhou; Huiyong Sun; Hui Liu; Dan Li 013; Huidong Yu; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2019)

ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches. - Zhenxing Wu; Tailong Lei; Chao Shen 008; Zhe Wang 041; Dong-Sheng Cao 001; Tingjun Hou (J. Chem. Inf. Model., 2019)

Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery. - Zi-Yi 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 001 (J. Chem. Inf. Model., 2019)

HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. - Gaoqi Weng; Ercheng Wang; Zhe Wang 041; Hui Liu; Feng Zhu 004; Dan Li 013; Tingjun Hou (Nucleic Acids Res., 2019)

Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. - Chao Shen 008; Zhe Wang 041; Xiaojun Yao; Youyong Li; Tailong Lei; Ercheng Wang; Lei Xu 035; Feng Zhu 004; Dan Li 013; Tingjun Hou (Briefings Bioinform., 2020)

Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning. - Jike Wang; Dong-Sheng Cao 001; Cunchen Tang; Xi Chen; Huiyong Sun; Tingjun Hou (Bioinform., 2020)

ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning. - Dejun Jiang 002; Tailong Lei; Zhe Wang 041; Chao Shen 008; Dong-Sheng Cao 001; Tingjun Hou (J. Cheminformatics, 2020)

Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis. - Li Fu; Lu Liu; Zhi-Jiang Yang; Pan Li; Jun-Jie Ding; Yong-Huan Yun; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2020)

Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities. - Ercheng Wang; Hui Liu; Junmei Wang; Gaoqi Weng; Huiyong Sun; Zhe Wang 041; Yu Kang 002; Tingjun Hou (J. Chem. Inf. Model., 2020)

Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays. - Zi-Yi Yang; Jie Dong; Zhi-Jiang Yang; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2020)

Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring. - Wenling Ye; Chao Shen 008; Guo-Li Xiong; Jun-Jie Ding; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2020)

BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study. - Jie Dong; Min-Feng Zhu; Yong-Huan Yun; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

QSAR-assisted-MMPA to expand chemical transformation space for lead optimization. - Li Fu; Zi-Yi Yang; Zhi-Jiang Yang; Mingzhu Yin; Ai-Ping Lu; Xiang Chen; Shao Liu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

Beware of the generic machine learning-based scoring functions in structure-based virtual screening. - Chao Shen 008; Ye Hu; Zhe Wang 041; Xujun Zhang; Jinping Pang; Gaoang Wang; Haiyang Zhong; Lei Xu 035; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions. - Chao Shen 008; Ye Hu; Zhe Wang 041; Xujun Zhang; Haiyang Zhong; Gaoang Wang; Xiaojun Yao; Lei Xu 035; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening? - Chao Shen 008; Gaoqi Weng; Xujun Zhang; Elaine Lai-Han Leung; Xiaojun Yao; Jinping Pang; Xin Chai; Dan Li 013; Ercheng Wang; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges. - Jike Wang; Dong-Sheng Cao 001; Cunchen Tang; Lei Xu 035; Qiaojun He; Bo Yang 023; Xi Chen; Huiyong Sun; Tingjun Hou (Briefings Bioinform., 2021)

Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method. - Zhenxing Wu; Dejun Jiang 002; Chang-Yu Hsieh; Guangyong Chen; Ben Liao; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets. - Zhenxing Wu; Minfeng Zhu; Yu Kang 002; Elaine Lai-Han Leung; Tailong Lei; Chao Shen 008; Dejun Jiang 002; Zhe Wang 041; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules. - Chengkun Wu; Xiao-Chen Zhang; Zhi-Jiang Yang; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

Improving structure-based virtual screening performance via learning from scoring function components. - Guo-Li Xiong; Wenling Ye; Chao Shen 008; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds. - Zi-Yi Yang; Jie Dong; Zhi-Jiang Yang; Mingzhu Yin; Hong-Li Jiang; Ai-Ping Lu; Xiang Chen; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

Scopy: an integrated negative design python library for desirable HTS/VS database design. - Zi-Yi Yang; Zhi-Jiang Yang; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

PySmash: Python package and individual executable program for representative substructure generation and application. - Zi-Yi Yang; Zhi-Jiang Yang; Yue Zhao; Mingzhu Yin; Ai-Ping Lu; Xiang Chen; Shao Liu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

Identification of active molecules against Mycobacterium tuberculosis through machine learning. - Qing Ye; Xin Chai; Dejun Jiang 002; Liu Yang; Chao Shen 008; Xujun Zhang; Dan Li 013; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction. - Xiao-Chen Zhang; Chengkun Wu; Zhi-Jiang Yang; Zhen-Xing Wu; Jiacai Yi; Chang-Yu Hsieh; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models. - Dejun Jiang 002; Zhenxing Wu; Chang-Yu Hsieh; Guangyong Chen; Ben Liao; Zhe Wang 041; Chao Shen 008; Dong-Sheng Cao 001; Jian Wu 001; Tingjun Hou (J. Cheminformatics, 2021)

The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction. - Chao Shen 008; Xueping Hu; Junbo Gao; Xujun Zhang; Haiyang Zhong; Zhe Wang 041; Lei Xu 035; Yu Kang 002; Dong-Sheng Cao 001; Tingjun Hou (J. Cheminformatics, 2021)

Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion. - Zi-Yi Yang; Li Fu; Ai-Ping Lu; Shao Liu; Tingjun Hou; Dong-Sheng Cao 001 (J. Cheminformatics, 2021)

ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions. - Xujun Zhang; Chao Shen 008; Xueying Guo; Zhe Wang 041; Gaoqi Weng; Qing Ye; Gaoang Wang; Qiaojun He; Bo Yang 023; Dong-Sheng Cao 001; Tingjun Hou (J. Cheminformatics, 2021)

VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations. - Ercheng Wang; Weitao Fu; Dejun Jiang 002; Huiyong Sun; Junmei Wang; Xujun Zhang; Gaoqi Weng; Hui Liu; Peng Tao 007; Tingjun Hou (J. Chem. Inf. Model., 2021)

CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. - Hongyan Du; Junbo Gao; Gaoqi Weng; Jun-Jie Ding; Xin Chai; Jinping Pang; Yu Kang 002; Dan Li 013; Dong-Sheng Cao 001; Tingjun Hou (Nucleic Acids Res., 2021)

PROTAC-DB: an online database of PROTACs. - Gaoqi Weng; Chao Shen 008; Dong-Sheng Cao 001; Junbo Gao; Xiaowu Dong; Qiaojun He; Bo Yang 023; Dan Li 013; Jian Wu 001; Tingjun Hou (Nucleic Acids Res., 2021)

ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. - Guo-Li Xiong; Zhenxing Wu; Jiacai Yi; Li Fu; Zhi-Jiang Yang; Chang-Yu Hsieh; Mingzhu Yin; Xiangxiang Zeng; Chengkun Wu; Ai-Ping Lu; Xiang Chen; Tingjun Hou; et al. (Nucleic Acids Res., 2021)

Multi-constraint molecular generation based on conditional transformer, knowledge distillation and reinforcement learning. - Jike Wang; Chang-Yu Hsieh; Mingyang Wang 004; Xiaorui Wang; Zhenxing Wu; Dejun Jiang 002; Benben Liao; Xujun Zhang; Bo Yang 023; Qiaojun He; Dongsheng Cao 001; Xi Chen; et al. (Nat. Mach. Intell., 2021)

DeepChargePredictor: a web server for predicting QM-based atomic charges via state-of-the-art machine-learning algorithms. - Jike Wang; Huiyong Sun; Jiawen Chen; Dejun Jiang 002; Zhe Wang 041; Zhenxing Wu; Xi Chen; Dong-Sheng Cao 001; Tingjun Hou (Bioinform., 2021)

Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning. - Dejun Jiang 002; Huiyong Sun; Jike Wang; Chang-Yu Hsieh; Yuquan Li; Zhenxing Wu; Dong-Sheng Cao 001; Jian Wu 001; Tingjun Hou (Briefings Bioinform., 2022)

Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations. - Rongfan Tang; Pengcheng Chen; Zhe Wang 041; Lingling Wang; Haiping Hao; Tingjun Hou; Huiyong Sun (Briefings Bioinform., 2022)

fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation. - Zhe Wang 041; Hong Pan; Huiyong Sun; Yu Kang 002; Huanxiang Liu; Dongsheng Cao 001; Tingjun Hou (Briefings Bioinform., 2022)

Comprehensive assessment of deep generative architectures for de novo drug design. - Mingyang Wang 004; Huiyong Sun; Jike Wang; Jinping Pang; Xin Chai; Lei Xu 035; Honglin Li 003; Dongsheng Cao 001; Tingjun Hou (Briefings Bioinform., 2022)

Knowledge-based BERT: a method to extract molecular features like computational chemists. - Zhenxing Wu; Dejun Jiang 002; Jike Wang; Xujun Zhang; Hongyan Du; Lurong Pan; Chang-Yu Hsieh; Dongsheng Cao 001; Tingjun Hou (Briefings Bioinform., 2022)

ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images. - Xiao-Chen Zhang; Jiacai Yi; Guo-Ping Yang; Chengkun Wu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2022)

MICER: a pre-trained encoder-decoder architecture for molecular image captioning. - Jiacai Yi; Chengkun Wu; Xiao-Chen Zhang; Xinyi Xiao; Yanlong Qiu; Wentao Zhao; Tingjun Hou; Dong-Sheng Cao 001 (Bioinform., 2022)

Root-aligned SMILES for Molecular Retrosynthesis Prediction. - Zipeng Zhong; Jie Song 011; Zunlei Feng; Tiantao Liu; Lingxiang Jia; Shaolun Yao; Min Wu; Tingjun Hou; Mingli Song (CoRR, 2022)

ReMODE: a deep learning-based web server for target-specific drug design. - Mingyang Wang 004; Jike Wang; Gaoqi Weng; Yu Kang 002; Peichen Pan; Dan Li 013; Yafeng Deng; Honglin Li 003; Chang-Yu Hsieh; Tingjun Hou (J. Cheminformatics, 2022)

Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes. - Ning-Ning Wang; Xiang-Gui Wang; Guo-Li Xiong; Zi-Yi Yang; Ai-Ping Lu; Xiang Chen; Shao Liu; Tingjun Hou; Dong-Sheng Cao 001 (J. Cheminformatics, 2022)

VGSC-DB: an online database of voltage-gated sodium channels. - Gaoang Wang; Jiahui Yu; Hongyan Du; Chao Shen 008; Xujun Zhang; Yifei Liu; Yangyang Zhang; Dong-Sheng Cao 001; Peichen Pan; Tingjun Hou (J. Cheminformatics, 2022)

Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses. - Yang Yu; Zhe Wang 041; Lingling Wang; Sheng Tian; Tingjun Hou; Huiyong Sun (J. Cheminformatics, 2022)

Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands. - Haiyi Chen; Rui Zhou; Jinping Pang; Yue Guo 008; Jiawen Chen; Yu Kang 002; Mojie Duan; Tingjun Hou (J. Chem. Inf. Model., 2022)

Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning. - Qinghua Wang; Zhe Wang 041; Sheng Tian; Lingling Wang; Rongfan Tang; Yang Yu; Jingxuan Ge; Tingjun Hou; Haiping Hao; Huiyong Sun (J. Chem. Inf. Model., 2022)

ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction. - Jialu Wu; Junmei Wang; Zhenxing Wu; Shengyu Zhang; Yafeng Deng; Yu Kang 002; Dong-Sheng Cao 001; Chang-Yu Hsieh; Tingjun Hou (J. Chem. Inf. Model., 2022)

Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation. - Yuwei Yang; Zhenxing Wu; Xiaojun Yao; Yu Kang 002; Tingjun Hou; Chang-Yu Hsieh; Huanxiang Liu (J. Chem. Inf. Model., 2022)

Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism. - Jiahui Yu; Jike Wang; Hong Zhao; Junbo Gao; Yu Kang 002; Dong-Sheng Cao 001; Zhe Wang 041; Tingjun Hou (J. Chem. Inf. Model., 2022)

DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety. - 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 001 (Nucleic Acids Res., 2022)

MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation. - Yiheng Zhu 002; Zhenqiu Ouyang; Ben Liao; Jialu Wu; Yixuan Wu; Chang-Yu Hsieh; Tingjun Hou; Jian Wu 001 (IJCAI, 2023)

Sample-efficient Multi-objective Molecular Optimization with GFlowNets. - Yiheng Zhu 002; Jialu Wu; Chaowen Hu; Jiahuan Yan; Chang-Yu Hsieh; Tingjun Hou; Jian Wu 001 (NeurIPS, 2023)

Recent advances in artificial intelligence for retrosynthesis. - Zipeng Zhong; Jie Song 011; Zunlei Feng; Tiantao Liu; Lingxiang Jia; Shaolun Yao; Tingjun Hou; Mingli Song (CoRR, 2023)

From molecules to scaffolds to functional groups: building context-dependent molecular representation via multi-channel learning. - Yue Wan; Jialu Wu; Tingjun Hou; Chang-Yu Hsieh; Xiaowei Jia (CoRR, 2023)

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. - Yuchen Sun; Xibing He; Tingjun Hou; Lianjin Cai; Viet Hoang Man; Junmei Wang (J. Comput. Chem., 2023)

Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method. - Yuchen Sun; Tingjun Hou; Xibing He; Viet Hoang Man; Junmei Wang (J. Comput. Chem., 2023)

Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. - Teng-Zhi Long; Shao-Hua Shi; Shao Liu; Ai-Ping Lu; Zhao-Qian Liu; Min Li 007; Tingjun Hou; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2023)

Learning on topological surface and geometric structure for 3D molecular generation. - Odin Zhang; Tianyue Wang; Gaoqi Weng; Dejun Jiang 002; Ning Wang; Xiaorui Wang; Huifeng Zhao; Jialu Wu; Ercheng Wang; Guangyong Chen; Yafeng Deng; Peichen Pan; et al. (Nat. Comput. Sci., 2023)

Efficient and accurate large library ligand docking with KarmaDock. - Xujun Zhang; Odin Zhang; Chao Shen 008; Wanglin Qu; Shicheng Chen; Hanqun Cao; Yu Kang 002; Zhe Wang 041; Ercheng Wang; Jintu Zhang; Yafeng Deng; Furui Liu; et al. (Nat. Comput. Sci., 2023)

Reducing false positive rate of docking-based virtual screening by active learning. - 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 001 (Briefings Bioinform., 2023)

Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors. - Dong Wang; Zhenxing Wu; Chao Shen 008; Lingjie Bao; Hao Luo; Zhe Wang 041; Hucheng Yao; De-Xin Kong; Cheng Luo; Tingjun Hou (Briefings Bioinform., 2023)

Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis. - Lingling Wang; Lei Xu 035; Zhe Wang 041; Tingjun Hou; Haiping Hao; Huiyong Sun (Briefings Bioinform., 2023)

CovInter: interaction data between coronavirus RNAs and host proteins. - Kuerbannisha Amahong; Wei Zhang 218; Ying Zhou; Song Zhang; Jiayi Yin; Fengcheng Li; Hong-Quan Xu; Tian-Ci Yan; Zi-Xuan Yue; Yu-Hong Liu; Tingjun Hou; Yunqing Qiu; et al. (Nucleic Acids Res., 2023)

DrugMAP: molecular atlas and pharma-information of all drugs. - Fengcheng Li; Jiayi Yin; Mingkun Lu; Minjie Mou; Zhaorong Li; Zhenyu Zeng; Ying Tan; Shanshan Wang; Xinyi Chu; Haibin Dai; Tingjun Hou; Su Zeng; et al. (Nucleic Acids Res., 2023)

PROTAC-DB 2.0: an updated database of PROTACs. - Gaoqi Weng; Xuanyan Cai; Dong-Sheng Cao 001; Hongyan Du; Chao Shen 008; Yafeng Deng; Qiaojun He; Bo Yang 023; Dan Li 013; Tingjun Hou (Nucleic Acids Res., 2023)

Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials. - Jintu Zhang; Haotian Zhang; Zhixin Qin; Yu Kang 002; Xin Hong; Tingjun Hou (J. Chem. Inf. Model., 2023)

Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning? - Shukai Gu; Chao Shen 008; Jiahui Yu; Hong Zhao; Huanxiang Liu; Liwei Liu; Rong Sheng; Lei Xu 035; Zhe Wang 041; Tingjun Hou; Yu Kang 002 (Briefings Bioinform., 2023)

Comprehensive assessment of nine target prediction web services: which should we choose for target fishing? - Kai-Yue Ji; Chong Liu; Zhao-Qian Liu; Yafeng Deng; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2023)

Improved GNNs for Log D7.4 Prediction by Transferring Knowledge from Low-Fidelity Data. - 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 001 (J. Chem. Inf. Model., 2023)

Deep Generation Model Guided by the Docking Score for Active Molecular Design. - Yuwei Yang; Chang-Yu Hsieh; Yu Kang 002; Tingjun Hou; Huanxiang Liu; Xiaojun Yao (J. Chem. Inf. Model., 2023)

Molecular Generation with Reduced Labeling through Constraint Architecture. - Jike Wang; Yundian Zeng; Huiyong Sun; Junmei Wang; Xiaorui Wang; Ruofan Jin; Mingyang Wang 004; Xujun Zhang; Dong-Sheng Cao 001; Xi Chen; Chang-Yu Hsieh; Tingjun Hou (J. Chem. Inf. Model., 2023)

RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction. - Yunxia Wang; Zhen Chen; Ziqi Pan; Shijie Huang; Jin Liu; Weiqi Xia; Hongning Zhang; Mingyue Zheng; Honglin Li 003; Tingjun Hou; Feng Zhu 004 (Nucleic Acids Res., 2023)

On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate. - Haiyi Chen; Yue Guo 008; Shengqing Ye; Jintu Zhang; Haotian Zhang; Na Liu; Rui Zhou; Tingjun Hou; Hongguang Xia; Yu Kang 002; Mojie Duan (J. Chem. Inf. Model., 2023)

TransFoxMol: predicting molecular property with focused attention. - Jian Gao; Zheyuan Shen; Yufeng Xie; Jialiang Lu; Yang Lu; Sikang Chen; Qingyu Bian; Yue Guo 008; Liteng Shen; Jian Wu 001; Binbin Zhou; Tingjun Hou; et al. (Briefings Bioinform., 2023)

ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions. - Xujun Zhang; Chao Shen 008; Tianyue Wang; Yafeng Deng; Yu Kang 002; Dan Li 013; Tingjun Hou; Peichen Pan (Briefings Bioinform., 2023)

ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling. - Odin Zhang; Jintu Zhang; Jieyu Jin; Xujun Zhang; Renling Hu; Chao Shen 008; Hanqun Cao; Hongyan Du; Yu Kang 002; Yafeng Deng; Furui Liu; Guangyong Chen; et al. (Nat. Mac. Intell., 2023)

CODD-Pred: A Web Server for Efficient Target Identification and Bioactivity Prediction of Small Molecules. - Xiaodan Yin; Xiaorui Wang; Yuquan Li; Jike Wang; Yuwei Wang 008; Yafeng Deng; Tingjun Hou; Huanxiang Liu; Pei Luo; Xiaojun Yao (J. Chem. Inf. Model., 2023)

Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets. - Zhe Wang 041; Haiyang Zhong; Jintu Zhang; Peichen Pan; Dong Wang; Huanxiang Liu; Xiaojun Yao; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2023)

MetaRF: attention-based random forest for reaction yield prediction with a few trails. - Kexin Chen 003; Guangyong Chen; Junyou Li; Yuansheng Huang; Ercheng Wang; Tingjun Hou; Pheng-Ann Heng (J. Cheminformatics, 2023)

In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences. - 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 001 (J. Cheminformatics, 2023)

TB-IECS: an accurate machine learning-based scoring function for virtual screening. - Xujun Zhang; Chao Shen 008; Dejun Jiang 002; Jintu Zhang; Qing Ye; Lei Xu 035; Tingjun Hou; Peichen Pan; Yu Kang 002 (J. Cheminformatics, 2023)

From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery. - Zhenxing Wu; Jihong Chen; Yitong Li; Yafeng Deng; Haitao Zhao; Chang-Yu Hsieh; Tingjun Hou (J. Chem. Inf. Model., 2023)

Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling. - Sutong Xiang; Zhe Wang 041; Rongfan Tang; Lingling Wang; Qinghua Wang; Yang Yu; Qirui Deng; Tingjun Hou; Haiping Hao; Huiyong Sun (J. Chem. Inf. Model., 2023)

Multiscale topology in interactomic network: from transcriptome to antiaddiction drug repurposing. - Hongyan Du; Guo-Wei Wei 001; Tingjun Hou (Briefings Bioinform., 2024)

AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences. - Ruofan Jin; Qing Ye; Jike Wang; Zheng Cao; Dejun Jiang 002; Tianyue Wang; Yu Kang 002; Wanting Xu; Chang-Yu Hsieh; Tingjun Hou (Briefings Bioinform., 2024)

Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency. - Tianyue Wang; Langcheng Wang; Xujun Zhang; Chao Shen 008; Odin Zhang; Jike Wang; Jialu Wu; Ruofan Jin; Donghao Zhou; Shicheng Chen; Liwei Liu; Xiaorui Wang; et al. (Briefings Bioinform., 2024)

Structure-based virtual screening of novel USP5 inhibitors targeting the zinc finger ubiquitin-binding domain. - Tianhao Wang; Jianbo Tong; Xing Zhang; Zhe Wang 041; Lei Xu 035; Peichen Pan; Tingjun Hou (Comput. Biol. Medicine, 2024)

In-depth theoretical modeling to explore the mechanism of TPX-0131 overcoming lorlatinib resistance to ALKL1196M/G1202R mutation. - Xing Zhang; Jianbo Tong; Tianhao Wang; Zhe Wang 041; Shukai Gu; Lei Xu 035; Tingjun Hou; Peichen Pan (Comput. Biol. Medicine, 2024)

Generative AI for Controllable Protein Sequence Design: A Survey. - Yiheng Zhu 002; Zitai Kong; Jialu Wu; Weize Liu; Yuqiang Han; Mingze Yin; Hongxia Xu; Chang-Yu Hsieh; Tingjun Hou (CoRR, 2024)

Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation. - Odin Zhang; Yufei Huang 002; Shichen Cheng; Mengyao Yu; Xujun Zhang; Haitao Lin; Yundian Zeng; Mingyang Wang 004; Zhenxing Wu; Huifeng Zhao; Zaixi Zhang; Chenqing Hua; et al. (CoRR, 2024)

AAVDiff: Experimental Validation of Enhanced Viability and Diversity in Recombinant Adeno-Associated Virus (AAV) Capsids through Diffusion Generation. - Lijun Liu; Jiali Yang; Jianfei Song; Xinglin Yang; Lele Niu; Zeqi Cai; Hui Shi; Tingjun Hou; Chang-Yu Hsieh; Weiran Shen; Yafeng Deng (CoRR, 2024)

Deep Lead Optimization: Leveraging Generative AI for Structural Modification. - Odin Zhang; Haitao Lin; Hui Zhang; Huifeng Zhao; Yufei Huang 002; Yuansheng Huang; Dejun Jiang 002; Chang-Yu Hsieh; Peichen Pan; Tingjun Hou (CoRR, 2024)

Token-Mol 1.0: Tokenized drug design with large language model. - Jike Wang; Rui Qin; Mingyang Wang 004; Meijing Fang; Yangyang Zhang; Yuchen Zhu; Qun Su; Qiaolin Gou; Chao Shen 008; Odin Zhang; Zhenxing Wu; Dejun Jiang 002; et al. (CoRR, 2024)

Multi-Modal CLIP-Informed Protein Editing. - Mingze Yin; Hanjing Zhou; Yiheng Zhu 002; Miao Lin; Yixuan Wu; Jialu Wu; Hongxia Xu; Chang-Yu Hsieh; Tingjun Hou; Jintai Chen; Jian Wu 001 (CoRR, 2024)

S2ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning. - Mingze Yin; Hanjing Zhou; Jialu Wu; Yiheng Zhu 002; Yuxuan Zhan; Zitai Kong; Hongxia Xu; Chang-Yu Hsieh; Jintai Chen; Tingjun Hou; Jian Wu 001 (CoRR, 2024)

RLpMIEC: High-Affinity Peptide Generation Targeting Major Histocompatibility Complex-I Guided and Interpreted by Interaction Spectrum-Navigated Reinforcement Learning. - Qirui Deng; Zhe Wang 041; Sutong Xiang; Qinghua Wang; Yifei Liu; Tingjun Hou; Huiyong Sun (J. Chem. Inf. Model., 2024)

Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. - Shukai Gu; Yuwei Yang; Yihao Zhao; Jiayue Qiu; Xiaorui Wang; Henry Hoi Yee Tong; Liwei Liu; Xiaozhe Wan; Huanxiang Liu; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2024)

TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides. - Nanqi Hong; Dejun Jiang 002; Zhe Wang 041; Huiyong Sun; Hao Luo; Lingjie Bao; Mingli Song; Yu Kang 002; Tingjun Hou (J. Chem. Inf. Model., 2024)

Discovery of Potent Covalent CRM1 Inhibitors Via a Customized Structure-Based Virtual Screening Pipeline and Bioassays. - He Liu; Chao Shen 008; Haonan Li; Tingjun Hou; Yongliang Yang 005 (J. Chem. Inf. Model., 2024)

DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery. - Chao Shen 008; Jianfei Song; Chang-Yu Hsieh; Dong-Sheng Cao 001; Yu Kang 002; Wenling Ye; Zhenxing Wu; Jike Wang; Odin Zhang; Xujun Zhang; Hao Zeng; Heng Cai; et al. (J. Chem. Inf. Model., 2024)

Characterizing the Cooperative Effect of PROTAC Systems with End-Point Binding Free Energy Calculation. - Kexin Xu; Zhe Wang 041; Sutong Xiang; Rongfan Tang; Qirui Deng; Jingxuan Ge; Zhiliang Jiang; Kaimo Yang; Tingjun Hou; Huiyong Sun (J. Chem. Inf. Model., 2024)

Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes. - Huifeng Zhao; Dejun Jiang 002; Chao Shen 008; Jintu Zhang; Xujun Zhang; Xiaorui Wang; Dou Nie; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2024)

Leveraging language model for advanced multiproperty molecular optimization via prompt engineering. - Zhenxing Wu; Odin Zhang; Xiaorui Wang; Li Fu; Huifeng Zhao; Jike Wang; Hongyan Du; Dejun Jiang 002; Yafeng Deng; Dong-Sheng Cao 001; Chang-Yu Hsieh; Tingjun Hou (Nat. Mac. Intell., 2024)

Dissecting the role of ALK double mutations in drug resistance to lorlatinib with in-depth theoretical modeling and analysis. - Xing Zhang; Jianbo Tong; Tianhao Wang; Tianyue Wang; Lei Xu 035; Zhe Wang 041; Tingjun Hou; Peichen Pan (Comput. Biol. Medicine, 2024)

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. - Mingyang Wang 004; Zhengjian Wu; Jike Wang; Gaoqi Weng; Yu Kang 002; Peichen Pan; Dan Li 013; Yafeng Deng; Xiaojun Yao; Zhitong Bing; Chang-Yu Hsieh; Tingjun Hou (J. Chem. Inf. Model., 2024)

A general model for predicting enzyme functions based on enzymatic reactions. - Wenjia Qian; Xiaorui Wang; Yu Kang 002; Peichen Pan; Tingjun Hou; Chang-Yu Hsieh (J. Cheminformatics, 2024)

Synergy of GFlowNet and Protein Language Model Makes a Diverse Antibody Designer. - Mingze Yin; Hanjing Zhou; Yiheng Zhu 002; Jialu Wu; Wei Wu 045; Mingyang Li; Kun Fu; Zheng Wang 027; Chang-Yu Hsieh; Tingjun Hou; Jian Wu 001 (AAAI, 2025)

Comprehensive Evaluation of End-Point Free Energy Methods in DNA-Ligand Interaction Predictions. - Cuiyu Li; Hongyan Du; Chengwei Zhang; Wanying Huang; Xujun Zhang; Tianyue Wang; Dejun Jiang 002; Tingjun Hou; Ercheng Wang (J. Chem. Inf. Model., 2025)

Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation. - Dou Nie; Huifeng Zhao; Odin Zhang; Gaoqi Weng; Hui Zhang; Jieyu Jin; Haitao Lin; Yufei Huang 002; Liwei Liu; Dan Li 013; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2025)

Deep Learning-Driven Insights into Enzyme-Substrate Interaction Discovery. - Wenjia Qian; Xiaorui Wang; Yuansheng Huang; Yu Kang 002; Peichen Pan; Chang-Yu Hsieh; Tingjun Hou (J. Chem. Inf. Model., 2025)

A Unified Deep Graph Model for Identifying the Molecular Categories of Ligands Targeting Nuclear Receptors. - Kaimo Yang; Dejun Jiang 002; Qirui Deng; Sutong Xiang; Jingxuan Ge; Kexin Xu; Zhiliang Jiang; Zihao Wang; Chen Yin; Youqiao Qian; Tingjun Hou; Huiyong Sun (J. Chem. Inf. Model., 2025)

PepPCBench is a Comprehensive Benchmarking Framework for Protein-Peptide Complex Structure Prediction. - Silong Zhai; Huifeng Zhao; Jike Wang; Shaolong Lin; Tiantao Liu; Shukai Gu; Dejun Jiang 002; Huanxiang Liu; Yu Kang 002; Xiaojun Yao; Tingjun Hou (J. Chem. Inf. Model., 2025)

Deep lead optimization enveloped in protein pocket and its application in designing potent and selective ligands targeting LTK protein. - Shicheng Chen; Odin Zhang; Chenran Jiang; Huifeng Zhao; Xujun Zhang; Mengting Chen; Yun Liu; Qun Su; Zhenxing Wu; Xinyue Wang; Wanglin Qu; Yuanyi Ye; et al. (Nat. Mac. Intell., 2025)

Benchmarking AI-powered docking methods from the perspective of virtual screening. - Shukai Gu; Chao Shen 008; Xujun Zhang; Huiyong Sun; Heng Cai; Hao Luo; Huifeng Zhao; Bo Liu; Hongyan Du; Yihao Zhao; Chenggong Fu; Silong Zhai; et al. (Nat. Mac. Intell., 2025)

ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings. - Zitai Kong; Yiheng Zhu 002; Yinlong Xu; Hanjing Zhou; Mingzhe Yin; Jialu Wu; Hongxia Xu; Chang-Yu Hsieh; Tingjun Hou; Jian Wu 001 (CoRR, 2025)

Graph Neural Networks in Modern AI-aided Drug Discovery. - Odin Zhang; Haitao Lin; Xujun Zhang; Xiaorui Wang; Zhenxing Wu; Qing Ye; Weibo Zhao; Jike Wang; Kejun Ying; Yu Kang 002; Chang-Yu Hsieh; Tingjun Hou (CoRR, 2025)

A Scalable and Quantum-Accurate Foundation Model for Biomolecular Force Field via Linearly Tensorized Quadrangle Attention. - Qun Su; Kai Zhu; Qiaolin Gou; Jintu Zhang; Renling Hu; Yurong Li; Yongze Wang; Hui Zhang; Ziyi You; Linlong Jiang; Yu Kang 002; Jike Wang; et al. (CoRR, 2025)

BioScore: A Foundational Scoring Function For Diverse Biomolecular Complexes. - Yuchen Zhu; Jihong Chen; Yitong Li; Xiaomin Fang; Xianbin Ye; Jingzhou He; Xujun Zhang; Jingxuan Ge; Chao Shen 008; Xiaonan Zhang; Tingjun Hou; Chang-Yu Hsieh (CoRR, 2025)

ADMET evaluation in drug discovery: 21. Application and industrial validation of machine learning algorithms for Caco-2 permeability prediction. - Dong Wang; Jieyu Jin; Guqin Shi; Jingxiao Bao; Zheng Wang 027; Shimeng Li; Peichen Pan; Dan Li 013; Yu Kang 002; Tingjun Hou (J. Cheminformatics, 2025)

Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates. - Xiaodan Yin; Xiaorui Wang; Zhenxing Wu; Qin Li; Yu Kang 002; Yafeng Deng; Pei Luo; Huanxiang Liu; Guqin Shi; Zheng Wang 027; Xiaojun Yao; Chang-Yu Hsieh; et al. (J. Cheminformatics, 2025)