| 1 |
Muhammad Shahid Malik , Van The Le , Yu-Yen Ou |
Enhancing the classification of metal-binding residue in proteins with retrieval-augmented generation, protein language models, and deep learning |
Engineering Applications of Artificial Intelligence |
2026 |
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| 2 |
Muhammad Shahid Malik , Muhammad Hussain, Quang-Thai Ho, Van-The Le , Yu-Yen Ou |
RAG-msCNN: predicting protein-DNA binding sites by integration of retrieval-augmented generation (RAG) with protein language models and the multi-scale separable convolutional neural network |
Biomedical Signal Processing and Control |
2026 |
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| 3 |
Van The Le, Muhammad Shahid Malik, Yu-Yen Ou |
DEEPTRANS: Enhancing primary active transport protein prediction via RAG-augmented protein language models and multi-scale deep learning |
Chemical Physics Letters |
2026 |
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| 4 |
Van The Le , Juan Peter Timothy Yuune , Thi Thu Phuong Vu , Muhammad Shahid Malik & Yu-Yen Ou |
DeepCR: predicting cytokine receptor proteins through pretrained language models and deep learning networks |
Journal of Biomolecular Structure and Dynamics |
2025 |
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| 5 |
Muhammad Shahid Malik, Van The Le, Yu-Yen Ou |
NA_mCNN: Classification of Sodium Transporters in Membrane Proteins by Integrating Multi-Window Deep Learning and ProtTrans for Their Therapeutic Potential |
Journal of Proteome Research |
2025 |
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| 6 |
Van-The Le, Yu-Chen Liu, Yan-Yun Chang, Yu-Cheng Lee, Yi-Jing Lin, Muhammad-Shahid Malik, Yu-Yen Ou |
NAD_MCNN: Combining Protein Language Models and Multiwindow Convolutional Neural Networks for Deacetylase NAD+ Binding Site Prediction |
Chemical Biology & Drug Design |
2025 |
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| 7 |
Syed Muazzam Ali Shah, Muhammad Rafi, Muhammad Shahid Malik, Sohail Ahmed Malik, Yu-Yen Ou. |
mCNN-glucose: Identifying families of glucose transporters using a deep convolutional neural network based on multiple-scanning windows |
International Journal of Biological Macromolecules |
2025 |
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| 8 |
Van-The Le, Muhammad-Shahid Malik , Yi-Jing Lin , Yu-Chen Liu , Yan-Yun Chang , Yu-Yen Ou |
ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networks |
Computers in Biology and Medicine |
2025 |
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| 9 |
Muhammad Shahid Malik, Van The Le, Syed Muazzam Ali Shah, & Yu-Yen Ou |
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 learning |
Journal Of Biomolecular Structure and Dynamics |
2024 |
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| 10 |
Van The Le, Yi-Hsuan Tseng, Yu-Chen Liu, Muhammad Shahid Malik, Yu-Yen Ou |
VesiMCNN: Using pre-trained protein language models and multiple window scanning convolutional neural networks to identify vesicular transport proteins |
International Journal of Biological Macromolecules |
2024 |
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| 11 |
Muhammad Shahid Malik, Yan-Yun Chang, Yu-Chen Liu, Van The Le, Yu-Yen Ou |
MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural Networks |
Journal of Chemical Information and Modeling |
2024 |
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| 12 |
VT Le, ZJ Zhan, Muhammad Shahid Malik, YY Ou |
ProtTrans and multi-window scanning convolutional neural networks for the prediction of protein-peptide interaction sites |
Journal of Molecular Graphics and Modelling |
2024 |
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| 13 |
VT Le, Muhammad Shahid Malik, YH Tseng, YC Lee, CI Huang, YY Ou |
DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language models |
Computational Biology and Chemistry |
2024 |
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| 14 |
Muhammad Shahid Malik, YY Ou |
Integrating Pre-Trained protein language model and multiple window scanning deep learning networks for accurate identification of secondary active transporters in membrane proteins |
Methods |
2023 |
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| 15 |
ZNK Swati, A Ghulam, M Sohail, JU Arshed, R Sikander, Muhammad Shahid Malik, Nauman khan |
XGboost-Ampy: Identification of AMPylation Protein Function Prediction Using Machine Learning |
VAWKUM Transactions on Computer Sciences |
2022 |
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| 16 |
S Rahu, A Ghulam, ZNK Swati, JU Arshed, Muhammad Shahid Malik, Nauman khan |
AOPs-XGBoost: Machine learning Model for the prediction of Antioxidant Proteins properties of peptides |
VAWKUM Transactions on Computer Sciences |
2022 |
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| 17 |
S Rahim, T Bibi, S Bahadur Qutoshi, S Gul, Y Gul, NAKK Khani, Muhammad Shahid Malik |
The challenges and opportunities to formulate and integrate an effective ict policy at mountainous rural schools of gilgit-baltistan |
Information |
2020 |
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