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2026

#1 2026 10

Prediction of intrinsic clearance using an explainable learning framework integrating molecular fingerprints and graph representation

作者: Jingnan Xu, Meiling Zhan, Mengyu Tong, Guixia Liu, Yun Tang, Weihua Li

期刊: European journal of medicinal chemistry

信息: 2026 | Vol.315 | 118996

#2 2026 09

ToxiCompass: an evidence-tracked benchmark for short-peptide toxicity screening and confidence-aware assay prioritization

作者: Qiule Yu, Zhixing Zhang, Weihua Li, Guixia Liu, Yun Tang

期刊: Briefings in bioinformatics

信息: 2026 | 27(5) | bbag526

#3 2026 09

AquaTox-Predictor: An MMoE-Enhanced Multimodal Deep Learning Framework for Aquatic Ecotoxicity Prediction

作者: Jingwei Zhang, Le Xiong, Fei Pan, Weihua Li, Xinxin Yu, Wenxiang Song, Dian Sheng, Yun Tang, Guixia Liu

期刊: Journal of chemical information and modeling

信息: 2026 | 66(18) | 11902-11915

#4 2026 07

HyperDC: A Non-Uniform Hypergraph Framework for Dual- and Higher-Order Drug Combination Recommendation Across Diverse Complex Diseases

作者: Hongbo Yu, Xinyi Chen, Wenxiang Song, Le Xiong, Xinmin Li, Ze Wang, Fei Pan, Weihua Li, Guixia Liu, Feng Gao, Yun Tang

期刊: Journal of chemical information and modeling

信息: 2026 | 66(14) | 8561-8578

#5 2026 06

MEG-mod: A Multiview Enhanced Graph Neural Network for Knockdown Efficiency Prediction of Chemically Modified siRNA

作者: Yuanting Chen, Mengyu Tong, Long Chen, Weihua Li, Keyun Zhu, Jiaying Li, Yun Tang, Guixia Liu

期刊: Journal of medicinal chemistry

信息: 2026 | 69(11) | 13434-13451

#6 2026 05

CypGEM: A Geometry-Aware and Edge-Enhanced Graph Transformer Model for Predicting Sites of Metabolism Mediated by Cytochromes P450

作者: Yuxin Zhang, Yingjie Yang, Meiling Zhan, Guixia Liu, Yun Tang, Weihua Li

期刊: Journal of chemical information and modeling

信息: 2026 | 66(10) | 5880-5896

#7 2026 05

ULCYP: A Multitask Model for Predicting P450 Inducers Based on Positive-Unlabeled Learning

作者: Changda Gong, Jiaojiao Fang, Guixia Liu, Yun Tang, Weihua Li

期刊: Journal of chemical information and modeling

信息: 2026 | 66(10) | 5838-5850

#8 2026 04

ncProFormer: A CNN-enhanced Transformer for ncRNA Coding-Potential Prediction

作者: Mengyu Tong, Yuanting Chen, Long Chen, Jingnan Xu, Yingjie Yang, Guixia Liu, Weihua Li, Yun Tang

期刊: Journal of chemical information and modeling

信息: 2026 | 66(7) | 3713-3724

#9 2026 04

EviCYP: In Silico Prediction of Cytochrome P450 Substrates Based on Vector Quantization and Evidential Deep Learning

作者: Yingjie Yang, Yuxin Zhang, Wenxiang Song, Keyun Zhu, Xinmin Li, Mengyu Tong, Guixia Liu, Weihua Li, Yun Tang

期刊: Journal of chemical information and modeling

信息: 2026 | 66(7) | 3892-3903

#10 2026 03

Chemotaxis-guided nanoplatform for non-alcoholic steatohepatitis therapy via macrophage reprogramming, hepatoprotection and gut microbiome modulation

作者: Xier Pan, Xinyi Chen, Ying Ma, Jiafeng Zou, Yiting Lin, Xinlin Zhao, Yanwen Wang, Yun Tang, Feng Gao

期刊: Biomaterials

信息: 2026 | Vol.326 | 123694

#11 2026 03

Vincamine as a GPR40 agonist shows potential in treating female Alzheimer's disease

作者: Jianlu Lyu, Danyang Zhu, Ze Wang, Jianqiao Fang, Yuanji Zhao, Lin Ma, Yun Tang, Jiaying Wang, Xu Shen

期刊: Phytomedicine : international journal of phytotherapy and phytopharmacology

信息: 2026 | Vol.152 | 157855

#12 2026 02

UGTformer: a pretrained graph transformer model for predicting UDP-glucuronosyltransferase-mediated drug metabolism

作者: Meiling Zhan, Xiang Li, Le Xiong, Wenxiang Song, Jiaojiao Fang, Guixia Liu, Yun Tang, Weihua Li

期刊: Journal of cheminformatics

信息: 2026 | 18(1) | 33

#13 2026 01

Prediction of Intravenous Pharmacokinetic Parameters across Multiple Species by a Multifidelity Deep Learning Framework

作者: Jiaojiao Fang, Changda Gong, Keyun Zhu, Xiang Li, Chen Yang, Zhixing Zhang, Guixia Liu, Yun Tang, Weihua Li

期刊: Journal of chemical information and modeling

信息: 2026 | 66(2) | 1035-1049

2025

#1 2025 12

SGEDiff: a subgraph-enriched diffusion model for structure-based 3D molecular generation

作者: Changda Gong, Jiaojiao Fang, Yan Tang, Guixia Liu, Yun Tang, Weihua Li

期刊: Journal of cheminformatics

信息: 2025 | 17(1) | 175

#2 2025 12

Computational Insights into the Regioselective Hydroxylation of Nirmatrelvir Metabolized by Cytochrome P450 3A4

作者: Yan Tang, Jiaojiao Fang, Guixia Liu, Yun Tang, Weihua Li

期刊: Journal of chemical information and modeling

信息: 2025 | 65(24) | 13346-13359

#3 2025 11

HerbComb: An integrated database for the discovery of novel combinational therapies from herbal medicines

作者: Yinyin Wang, Rui Liu, Xiang Luo, Jiaqi Yao, Hao Liu, Chengyuan Yue, Boon Seng Kho, Xiaochuang Xu, Shixing Lai, Fangcheng Yu, Yinnan Zhang, Lin Cao, Ninghua Tan, Yun Tang, Tao Yang, Jing Tang

期刊: Computational and structural biotechnology journal

信息: 2025 | Vol.27 | 4915-4935

#4 2025 11

Cocrystal Network-Based Recommendation: a multi-objective random walk-based network model for virtual screening of drug-drug cocrystals

作者: Song WX#, Wu J#, Zhou CD#, Huang SW, She BG, Liu GX, Li WH, Ren GB, Zhu B*, Tang Y*

期刊: Journal of Medicinal Chemistry

信息: 2025 | 68(21) | 22831-22844

#5 2025 11

KG-CNNDTI: A knowledge graph-enhanced prediction model for drug-target interactions and demonstrated in drug screening for anti-Alzheimer’s disease

作者: Yue CY#, Chen BY#, Chen L, Xiong L, Gong CD, Wang Z, Liu GX, Li WH, Wang R*, Tang Y*

期刊: Chinese Journal of Natural Medicines

信息: 2025 | 23(11) | 1283-1292

#6 2025 10

ACtriplet: an improved deep learning model for activity cliffs prediction by integrating triplet loss and pre-training

作者: Yu XX, Wang YM, Chen L, Li WH, Tang Y*, Liu GX*

期刊: Journal of Pharmaceutical Analysis

信息: 2025 | 15(8) | 101317

#7 2025 09

ComplexDnet: a network-based strategy to discover critical targets and screen active compounds for complex diseases

作者: Pan F#, Xu ZM#, Liu ZH, Chen CY, Yu JW, Wu ZR, Wang Z, Chen L, Yue CY, Li WH, Liu GX, Huang J*, Tang Y*

期刊: Journal of Medicinal Chemistry

信息: 2025 | 68(18) | 19463-19481

#8 2025 09

BBANsh: A deep learning architecture based on BERT and bilinear attention networks to identify potent shRNA

作者: Chen YT, Chen L, Yu XX, Li WH, Tang Y*, Liu GX*

期刊: Briefings in Bioinformatics

信息: 2025 | 26(4) | bbaf443

#9 2025 08

MMPK: a multimodal deep learning framework to predict human oral pharmacokinetic parameters

作者: Li X, Zhan ML, Fang JJ, Liu GX, Tang Y*, Li WH*

期刊: Journal of Medicinal Chemistry

信息: 2025 | 68(15) | 16678-16690

#10 2025 08

CLaSP: a contrastive learning-guided latent scoring platform for comprehensive drug-likeness evaluation

作者: Li XM, Chen L, Yu HB, Xiong L, Song WX, Li X, Liu GX, Li WH, Tang Y*

期刊: Journal of Medicinal Chemistry

信息: 2025 | 68(15) | 16750-16765

#11 2025 06

In Silico Prediction of pKa Values Using Explainable Deep Learning Methods

作者: Chen Yang, Changda Gong, Zhixing Zhang, Jiaojiao Fang, Weihua Li, Guixia Liu, Yun Tang

期刊: Journal of Pharmaceutical Analysis

信息: 2025 | 15(6) | 101174

#12 2025 06

ERRα-Predictor: A Framework of Ensemble Models for Prediction of ERRα Binders, Antagonists, and Agonists Using Artificial Intelligence

作者: Le Xiong, Jiahao Xu, Hongbo Yu, Weihua Li, Xinmin Li, Wenxiang Song, Jingwei Zhang, Yun Tang*, Guixia Liu*

期刊: Journal of Chemical Information and Modeling

信息: 2025 | 65(13) | 6809–6822

#13 2025 04

TCnet: a novel strategy to predict target combination of Alzheimer’s disease via network-based methods

作者: Yue CY, Chen BY, Pan F, Wang Z, Yu HB, Liu GX, Li WH, Wang R*, Tang Y*

期刊: Journal of Chemical Information and Modeling

信息: 2025 | 65(7) | 3866-3878

#14 2025 03

Fluor-Predictor: An Interpretable Tool for Multiproperty Prediction and Retrieval of Fluorescent Dyes

作者: Wenxiang Song, Le Xiong, Xinmin Li, Yuyang Zhang, Binya Wang, Guixia Liu, Weihua Li, Youjun Yang*, Yun Tang*

期刊: Journal of Chemical Information and Modeling

信息: 2025 | 65(6) | 2854-2867

#15 2025 03

Cocry-pred: a dynamic resource propagation method for cocrystal prediction

作者: Song WX#, Peng R#, Yu HB, Zhan ML, Liu GX, Li WH, Ren GB, Zhu B*, Tang Y*

期刊: Journal of Chemical Information and Modeling

信息: 2025 | 65(6) | 2868-2881

#16 2025 01

GCLmf: A Novel Molecular Graph Contrastive Learning Framework Based on Hard Negatives and Application in Toxicity Prediction

作者: Xinxin Yu, Yuanting Chen, Long Chen, Weihua Li, Yuhao Wang, Yun Tang, Guixia Liu

期刊: Molecular informatics

信息: 2025 | 44(1) | e202400169

#17 2025

Fluor-tools: an integrated platform for dye property prediction and structure optimization

作者: Song, W.; Zhang, Y.; Xiong, L.; Li, X.; Zhang, J.; Liu, G.; Li, W.; Yang, Y.; Tang, Y.

期刊: Digital Discovery

信息: 2025

发表论文

2026

Prediction of intrinsic clearance using an explainable learning framework integrating molecular fingerprints and graph representation

ToxiCompass: an evidence-tracked benchmark for short-peptide toxicity screening and confidence-aware assay prioritization

AquaTox-Predictor: An MMoE-Enhanced Multimodal Deep Learning Framework for Aquatic Ecotoxicity Prediction

HyperDC: A Non-Uniform Hypergraph Framework for Dual- and Higher-Order Drug Combination Recommendation Across Diverse Complex Diseases

MEG-mod: A Multiview Enhanced Graph Neural Network for Knockdown Efficiency Prediction of Chemically Modified siRNA

CypGEM: A Geometry-Aware and Edge-Enhanced Graph Transformer Model for Predicting Sites of Metabolism Mediated by Cytochromes P450

ULCYP: A Multitask Model for Predicting P450 Inducers Based on Positive-Unlabeled Learning

ncProFormer: A CNN-enhanced Transformer for ncRNA Coding-Potential Prediction

EviCYP: In Silico Prediction of Cytochrome P450 Substrates Based on Vector Quantization and Evidential Deep Learning

Chemotaxis-guided nanoplatform for non-alcoholic steatohepatitis therapy via macrophage reprogramming, hepatoprotection and gut microbiome modulation

Vincamine as a GPR40 agonist shows potential in treating female Alzheimer's disease

UGTformer: a pretrained graph transformer model for predicting UDP-glucuronosyltransferase-mediated drug metabolism

Prediction of Intravenous Pharmacokinetic Parameters across Multiple Species by a Multifidelity Deep Learning Framework

2025

SGEDiff: a subgraph-enriched diffusion model for structure-based 3D molecular generation

Computational Insights into the Regioselective Hydroxylation of Nirmatrelvir Metabolized by Cytochrome P450 3A4

HerbComb: An integrated database for the discovery of novel combinational therapies from herbal medicines

Cocrystal Network-Based Recommendation: a multi-objective random walk-based network model for virtual screening of drug-drug cocrystals

KG-CNNDTI: A knowledge graph-enhanced prediction model for drug-target interactions and demonstrated in drug screening for anti-Alzheimer’s disease

ACtriplet: an improved deep learning model for activity cliffs prediction by integrating triplet loss and pre-training

ComplexDnet: a network-based strategy to discover critical targets and screen active compounds for complex diseases

BBANsh: A deep learning architecture based on BERT and bilinear attention networks to identify potent shRNA

MMPK: a multimodal deep learning framework to predict human oral pharmacokinetic parameters

CLaSP: a contrastive learning-guided latent scoring platform for comprehensive drug-likeness evaluation

In Silico Prediction of pKa Values Using Explainable Deep Learning Methods

ERRα-Predictor: A Framework of Ensemble Models for Prediction of ERRα Binders, Antagonists, and Agonists Using Artificial Intelligence

TCnet: a novel strategy to predict target combination of Alzheimer’s disease via network-based methods

Fluor-Predictor: An Interpretable Tool for Multiproperty Prediction and Retrieval of Fluorescent Dyes

Cocry-pred: a dynamic resource propagation method for cocrystal prediction

GCLmf: A Novel Molecular Graph Contrastive Learning Framework Based on Hard Negatives and Application in Toxicity Prediction

Fluor-tools: an integrated platform for dye property prediction and structure optimization

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