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Muhammad Shahid Malik

Observed names: Muhammad-Shahid Malik, Muhammad‐Shahid Malik
ORCID: 0000-0001-5615-9000
Observed ORCID: 0000-0001-5615-9000
OpenAlex ID: A5007239930
Integrating Pre-Trained protein language model and multiple window scanning deep learning networks for accurate identification of secondary active transporters in membrane proteins
2023 · Muhammad Shahid Malik, Yu-Yen Ou · Methods · 23
ProtTrans and multi-window scanning convolutional neural networks for the prediction of protein-peptide interaction sites
2024 · Van-The Le, Zi-Jun Zhan, et al. · Journal of Molecular Graphics and Modelling · 15
DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language models
2024 · Van-The Le, Muhammad-Shahid Malik, et al. · Computational Biology and Chemistry · 12
MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural Networks
2024 · Muhammad Shahid Malik, Yan-Yun Chang, et al. · Journal of Chemical Information and Modeling · 8
ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networks
2024 · Van-The Le, Muhammad-Shahid Malik, et al. · Computers in Biology and Medicine · 6
VesiMCNN: Using pre-trained protein language models and multiple window scanning convolutional neural networks to identify vesicular transport proteins
2024 · Van The Le, Yi-Hsuan Tseng, et al. · International Journal of Biological Macromolecules · 5
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
2025 · Muhammad Shahid Malik, Muhammad Hussain, et al. · Biomedical Signal Processing and Control · 3
NA_mCNN: Classification of Sodium Transporters in Membrane Proteins by Integrating Multi-Window Deep Learning and ProtTrans for Their Therapeutic Potential
2025 · Muhammad Shahid Malik, Van The Le, et al. · Journal of Proteome Research · 2
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NAD_MCNN: Combining Protein Language Models and Multiwindow Convolutional Neural Networks for Deacetylase NAD + Binding Site Prediction
2025 · Van‐The Le, Yu‐Chen Liu, et al. · Chemical Biology & Drug Design · 2
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
2024 · Muhammad Shahid Malik, Van The Le, et al. · Journal of Biomolecular Structure and Dynamics · 2
Enhancing the classification of metal-binding residue in proteins with retrieval-augmented generation, protein language models, and deep learning
2026 · Muhammad Shahid Malik, Van The Le, et al. · Engineering Applications of Artificial Intelligence · 1
DeepCR: predicting cytokine receptor proteins through pretrained language models and deep learning networks
2025 · Van The Le, Juan Peter Timothy Yuune, et al. · Journal of Biomolecular Structure and Dynamics · 1
AOPs-XGBoost: Machine learning Model for the prediction of Antioxidant Proteins properties of peptides
2022 · Sikander Rahu, Ali Ghulam, et al. · VAWKUM Transactions on Computer Sciences · 1
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XGboost-Ampy: Identification of AMPylation Protein Function Prediction Using Machine Learning
2022 · Zar Nawab Khan Swati, Ali Ghulam, et al. · VAWKUM Transactions on Computer Sciences · 1
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mCNN-glucose: Identifying families of glucose transporters using a deep convolutional neural network based on multiple-scanning windows
2025 · Syed Muazzam Ali Shah, Muhammad Rafi, et al. · International Journal of Biological Macromolecules
Works count: 15
Citation count: 82
H-index: 5
I10-index: 3
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