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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)