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Journal of Proteome Research|April 7, 2025
NA_mCNN: Classification of Sodium Transporters in Membrane Proteins by Integrating Multi-Window Deep Learning and ProtTrans for Their Therapeutic PotentialMuhammad Shahid Malik, Van The Le, Yu-Yen OuJournal of Chemical Information and Modeling|December 31, 2025
IFNg_DeepKG: A Novel Model for Identifying Interferon-Gamma-Inducing Epitopes Using Knowledge Graph RAG in Biomedical ApplicationsVan The Le, Juan Peter Timothy Yuune, Yu-Yen OuJournal of Biomolecular Structure & Dynamics|November 22, 2024
MCNN-AAPT: accurate classification and functional prediction of amino acid and peptide transporters in secondary active transporters using protein language models and multi-window deep learningMuhammad Shahid Malik, Van The Le, Syed Muazzam Ali Shah, et al.Journal of Chemical Information and Modeling|August 12, 2024
MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural NetworksMuhammad Shahid Malik, Yan-Yun Chang, Yu-Chen Liu, et al.International Journal of Biological Macromolecules|September 27, 2024
VesiMCNN: Using pre-trained protein language models and multiple window scanning convolutional neural networks to identify vesicular transport proteinsVan The Le, Yi-Hsuan Tseng, Yu-Chen Liu, et al.Journal of Molecular Graphics & Modelling|April 20, 2024
ProtTrans and multi-window scanning convolutional neural networks for the prediction of protein-peptide interaction sitesVan-The Le, Zi-Jun Zhan, Thi-Thu-Phuong Vu, et al.Journal of Biomolecular Structure & Dynamics|May 31, 2025
DeepCR: predicting cytokine receptor proteins through pretrained language models and deep learning networksVan The Le, Juan Peter Timothy Yuune, Thi Thu Phuong Vu, et al.ACS Omega|December 8, 2025
CFTR_TL: Transfer Learning-Enhanced Prediction of CFTR ATP Binding Sites with Multi-Window Convolutional Neural NetworksYu-Cheng Lee, Yan-Yun Chang, Wei-En Jhang, et al.Computers in Biology and Medicine|December 9, 2024
ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networksVan-The Le, Muhammad-Shahid Malik, Yi-Jing Lin, et al.Computational Biology and Chemistry|March 31, 2024
DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language modelsVan-The Le, Muhammad-Shahid Malik, Yi-Hsuan Tseng, et al.Pageof 2