Diagnosing Breast Cancer Based on Support Vector Machines. - Huanxiang Liu; Ruisheng Zhang; Feng Luan; Xiaojun Yao; Mancang Liu; Zhide Hu; Bo Tao Fan (J. Chem. Inf. Comput. Sci., 2003)

QSAR Study of Ethyl 2-[(3-Methyl-2, 5-dioxo(3-pyrrolinyl))amino]-4-(trifluoromethyl) pyrimidine-5-carboxylate: An Inhibitor of AP-1 and NF-B Mediated Gene Expression Based on Support Vector Machines. - Huanxiang Liu; Ruisheng Zhang; Xiaojun Yao; Mancang Liu; Zhide Hu; Bo Tao Fan (J. Chem. Inf. Comput. Sci., 2003)

QSAR and classification models of a novel series of COX-2 selective inhibitors: 1, 5-diarylimidazoles based on support vector machines. - Huanxiang Liu; Ruisheng Zhang; Xiaojun Yao; Mancang Liu; Zhide Hu; Bo Tao Fan (J. Comput. Aided Mol. Des., 2004)

Quantitative Prediction of logk of Peptides in High-Performance Liquid Chromatography Based on Molecular Descriptors by Using the Heuristic Method and Support Vector Machine. - Huanxiang Liu; C. X. Xue; Ruisheng Zhang; Xiaojun Yao; Mancang Liu; Zhide Hu; Bo Tao Fan (J. Chem. Inf. Model., 2004)

Prediction of the Isoelectric Point of an Amino Acid Based on GA-PLS and SVMs. - Huanxiang Liu; Ruisheng Zhang; Xiaojun Yao; Mancang Liu; Zhide Hu; Bo Tao Fan (J. Chem. Inf. Model., 2004)

Support Vector Machines-Based Quantitative Structure-Property Relationship for the Prediction of Heat Capacity. - C. X. Xue; Ruisheng Zhang; Huanxiang Liu; Mancang Liu; Zhide Hu; Bo Tao Fan (J. Chem. Inf. Model., 2004)

An Accurate QSPR Study of O-H Bond Dissociation Energy in Substituted Phenols Based on Support Vector Machines. - C. X. Xue; Ruisheng Zhang; Huanxiang Liu; Xiaojun Yao; Mancang Liu; Zhide Hu; Bo Tao Fan (J. Chem. Inf. Model., 2004)

QSAR Models for the Prediction of Binding Affinities to Human Serum Albumin Using the Heuristic Method and a Support Vector Machine. - C. X. Xue; Ruisheng Zhang; Huanxiang Liu; Xiaojun Yao; Mancang Liu; Zhide Hu; Bo Tao Fan (J. Chem. Inf. Model., 2004)

Diagnosing Anorexia Based on Partial Least Squares, Back Propagation Neural Network, and Support Vector Machines. - C. Y. Zhao; Ruisheng Zhang; Huanxiang Liu; C. X. Xue; S. G. Zhao; X. F. Zhou; Mancang Liu; Bo Tao Fan (J. Chem. Inf. Model., 2004)

The prediction of human oral absorption for diffusion rate-limited drugs based on heuristic method and support vector machine. - Huanxiang Liu; Rongjing Hu; Ruisheng Zhang; Xiaojun Yao; Mancang Liu; Zhide Hu; Bo Tao Fan (J. Comput. Aided Mol. Des., 2005)

Prediction of the tissue/blood partition coefficients of organic compounds based on the molecular structure using least-squares support vector machines. - Huanxiang Liu; Xiaojun Yao; Ruisheng Zhang; Mancang Liu; Zhide Hu; Bo Tao Fan (J. Comput. Aided Mol. Des., 2005)

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of thiazolone derivatives as hepatitis C virus NS5B polymerase allosteric inhibitors. - Beilei Lei; Juan Du 003; Shuyan Li; Huanxiang Liu; Yueying Ren; Xiaojun Yao (J. Comput. Aided Mol. Des., 2008)

QSAR study of malonyl-CoA decarboxylase inhibitors using GA-MLR and a new strategy of consensus modeling. - Jiazhong Li; Beilei Lei; Huanxiang Liu; Shuyan Li; Xiaojun Yao; Mancang Liu; Paola Gramatica (J. Comput. Chem., 2008)

A novel method for protein-ligand binding affinity prediction and the related descriptors exploration. - Shuyan Li; Lili Xi; Chengqi Wang; Jiazhong Li; Beilei Lei; Huanxiang Liu; Xiaojun Yao (J. Comput. Chem., 2009)

Structure-based quantitative structure-activity relationship studies of checkpoint kinase 1 inhibitors. - Juan Du 003; Lili Xi; Beilei Lei; Jing Lu; Jiazhong Li; Huanxiang Liu; Xiaojun Yao (J. Comput. Chem., 2010)

A new strategy to improve the predictive ability of the local lazy regression and its application to the QSAR study of melanin-concentrating hormone receptor 1 antagonists. - Jiazhong Li; Shuyan Li; Beilei Lei; Huanxiang Liu; Xiaojun Yao; Mancang Liu; Paola Gramatica (J. Comput. Chem., 2010)

A combined molecular modeling study on gelatinases and their potent inhibitors. - Lili Xi; Juan Du 003; Shuyan Li; Jiazhong Li; Huanxiang Liu; Xiaojun Yao (J. Comput. Chem., 2010)

Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. - Iurii Sushko; Sergii Novotarskyi; Robert Körner; Anil Kumar Pandey; Artem Cherkasov; Jiazhong Li; Paola Gramatica; Katja Hansen; Timon Schroeter; Klaus-Robert Müller; Lili Xi; Huanxiang Liu; et al. (J. Chem. Inf. Model., 2010)

Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation. - Juan Du 003; Huijun Sun; Lili Xi; Jiazhong Li; Ying Yang; Huanxiang Liu; Xiaojun Yao (J. Comput. Chem., 2011)

In silico prediction of deleterious single amino acid polymorphisms from amino acid sequence. - Shuyan Li; Lili Xi; Jiazhong Li; Chengqi Wang; Beilei Lei; Yulin Shen; Huanxiang Liu; Xiaojun Yao; Biao Li (J. Comput. Chem., 2011)

Molecular Dynamics Simulation, Free Energy Calculation and Structure-Based 3D-QSAR Studies of B-RAF Kinase Inhibitors. - Ying Yang; Jin Qin; Huanxiang Liu; Xiaojun Yao (J. Chem. Inf. Model., 2011)

Molecular Dynamics Simulation and Free Energy Calculation Studies of the Binding Mechanism of Allosteric Inhibitors with p38α MAP Kinase. - Ying Yang; Yulin Shen; Huanxiang Liu; Xiaojun Yao (J. Chem. Inf. Model., 2011)

A sequence-based computational model for the prediction of the solvent accessible surface area for α-helix and β-barrel transmembrane residues. - Chengqi Wang; Lili Xi; Shuyan Li; Huanxiang Liu; Xiaojun Yao (J. Comput. Chem., 2012)

Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective. - Weiwei Xue; Huanxiang Liu; Xiaojun Yao (J. Comput. Chem., 2012)

Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis. - Weiwei Xue; Xiaojie Jin; Lulu Ning; Meixia Wang; Huanxiang Liu; Xiaojun Yao (J. Chem. Inf. Model., 2013)

Computational Study on the Drug Resistance Mechanism against HCV NS3/4A Protease Inhibitors Vaniprevir and MK-5172 by the Combination Use of Molecular Dynamics Simulation, Residue Interaction Network, and Substrate Envelope Analysis. - Weiwei Xue; Yihe Ban; Huanxiang Liu; Xiaojun Yao (J. Chem. Inf. Model., 2014)

In Silico Identification of Protein S-Palmitoylation Sites and Their Involvement in Human Inherited Disease. - Shuyan Li; Jiazhong Li; Lulu Ning; Shaopeng Wang; Yuzhen Niu; Nengzhi Jin; Xiaojun Yao; Huanxiang Liu; Lili Xi (J. Chem. Inf. Model., 2015)

Molecular mechanism of R-bicalutamide switching from androgen receptor antagonist to agonist induced by amino acid mutations using molecular dynamics simulations and free energy calculation. - Hongli Liu; Rui Han; Jiazhong Li; Huanxiang Liu; Lifang Zheng (J. Comput. Aided Mol. Des., 2016)

Discovery of small molecules binding to the normal conformation of prion by combining virtual screening and multiple biological activity evaluation methods. - Lanlan Li; Wei Wei; Wen-Juan Jia 002; Yongchang Zhu; Yan Zhang; Jiang-Huai Chen; Jiaqi Tian; Huanxiang Liu; Yong-Xing He; Xiaojun Yao (J. Comput. Aided Mol. Des., 2017)

The improved learning rate for regularized regression with RKBSs. - Huanxiang Liu; Baohuai Sheng; Peixin Ye (Int. J. Mach. Learn. Cybern., 2017)

Are the Apo Proteins Suitable for the Rational Discovery of Allosteric Drugs? - Xiaoli An; Shaoyong Lu; Kun Song 003; Qiancheng Shen; Meilan Huang; Xiaojun Yao; Huanxiang Liu; Jian Zhang 037 (J. Chem. Inf. Model., 2019)

Carbon Nanoparticles Inhibit the Aggregation of Prion Protein as Revealed by Experiments and Atomistic Simulations. - Shuangyan Zhou; Yongchang Zhu; Xiaojun Yao; Huanxiang Liu (J. Chem. Inf. Model., 2019)

MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm. - Qifeng Bai; Shuoyan Tan; Tingyang Xu; Huanxiang Liu; Junzhou Huang; Xiaojun Yao (Briefings Bioinform., 2021)

TrimNet: learning molecular representation from triplet messages for biomedicine. - Pengyong Li; Yuquan Li; Chang-Yu Hsieh; Shengyu Zhang 002; Xianggen Liu; Huanxiang Liu; Sen Song; Xiaojun Yao (Briefings Bioinform., 2021)

Discovery of novel IDO1 inhibitors via structure-based virtual screening and biological assays. - Huizhen Ge; Longfei Mao; Jie Zhao; Yuwei Wang 008; Danfeng Shi; Xing Yang; Xiaorui Wang; Huanxiang Liu; Xiaojun Yao (J. Comput. Aided Mol. Des., 2021)

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)

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)

An adaptive graph learning method for automated molecular interactions and properties predictions. - Yuquan Li; Chang-Yu Hsieh; Ruiqiang Lu; Xiaoqing Gong; Xiaorui Wang; Pengyong Li; Shuo Liu; Yanan Tian; Dejun Jiang 002; Jiaxian Yan; Qifeng Bai; Huanxiang Liu; et al. (Nat. Mach. Intell., 2022)

Predicting molecular properties based on the interpretable graph neural network with multistep focus mechanism. - Yanan Tian; Xiaorui Wang; Xiaojun Yao; Huanxiang Liu; Ying Yang (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)

Bioinformatics toolbox for exploring target mutation-induced drug resistance. - Yuan-Qin Huang; Ping Sun; Yi Chen; Huanxiang Liu; Ge-Fei Hao; Bao-An Song (Briefings Bioinform., 2023)

Improving drug-target affinity prediction via feature fusion and knowledge distillation. - Ruiqiang Lu; Jun Wang 123; Pengyong Li; Yuquan Li; Shuoyan Tan; Yiting Pan; Huanxiang Liu; Peng Gao 015; Guotong Xie; Xiaojun Yao (Briefings Bioinform., 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)

MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein-protein interactions. - Yang Yue; Shu Li; Lingling Wang; Huanxiang Liu; Henry H. Y. Tong; Shan He (Briefings Bioinform., 2023)

HF-DDI: Predicting Drug-Drug Interaction Events Based on Multimodal Hybrid Fusion. - An Huang; Xiaolan Xie; Xiaojun Yao; Huanxiang Liu; Xiaoqi Wang; Shaoliang Peng (J. Comput. Biol., 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)

Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays. - Qianqian Zhang; Jianting Han; Yongchang Zhu; Fansen Yu; Xiaopeng Hu; Henry H. Y. Tong; Huanxiang Liu (J. Comput. Aided Mol. Des., 2023)

Quick-MIMIC: A Multimodal Data Extraction Pipeline for MIMIC with Parallelization. - Yutao Dou; Wei Li; Yangtao Zheng; Xiaojun Yao; Huanxiang Liu; Albert Y. Zomaya; Shaoliang Peng (Big Data Min. Anal., 2024)

3DSGIMD: An accurate and interpretable molecular property prediction method using 3D spatial graph focusing network and structure-based feature fusion. - Yanan Tian; Chenbin Wang; Ruiqiang Lu; Henry H. Y. Tong; Xiaoqing Gong; Jiayue Qiu; Shaoliang Peng; Xiaojun Yao; Huanxiang Liu (Future Gener. Comput. Syst., 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)

Versatile Framework for Drug-Target Interaction Prediction by Considering Domain-Specific Features. - Shuo Liu; Jialiang Yu; Ningxi Ni; Zidong Wang 010; Mengyun Chen; Yuquan Li; Chen Xu; Yahao Ding; Jun Zhang 071; Xiaojun Yao; Huanxiang Liu (J. Chem. Inf. Model., 2024)

Elucidating the Selective Mechanism of Drugs Targeting Cyclin-Dependent Kinases with Integrated MetaD-US Simulation. - Lingling Wang; Shu Li; Sutong Xiang; Huanxiang Liu; Huiyong Sun (J. Chem. Inf. Model., 2024)

A Specialized and Enhanced Deep Generation Model for Active Molecular Design Targeting Kinases Guided by Affinity Prediction Models and Reinforcement Learning. - Xiaomeng Liu; Qin Li; Xiao Yan; Lingling Wang; Jiayue Qiu; Xiaojun Yao; Huanxiang Liu (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)

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)

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)