AlphaFold2-aware protein–DNA binding site prediction using graph transformer

Cited by (137)

Items 101–137 of 137

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5. AlphaFold meets de novo drug design: leveraging structural protein information in multi-target molecular generative models
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6. Genome-scale annotation of protein binding sites via language model and geometric deep learning
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7. Exploring Protein-DNA Binding Residue Prediction and Consistent Interpretability Analysis Using Deep Learning
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10. Dynamic Reachability Distance-Based Dense Clustering Method for Protein-DNA Sites Noise Reduction Based on the Predicted Binding Site Probabilities
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12. Utilizing Large Language Models and Graph Neural Networks for Protein–Protein Interaction Prediction and Isozyme Estimation
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15. ChaiSite: An Accurate Method for Protein–Nucleic Acid Binding Site Prediction Based on a Complex Structure Prediction Network
    Yi Li, Wenwu Zeng, Xiaolan Xie, Feng Hu, H. Xuanpengfan Zou, Shaoliang Peng · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
16. Overcoming Class Imbalance in Protein-Protein Interaction and Isozyme Prediction: GAN-Based Augmentation in a Transformer-GNN Framework
    Raghad J. AbuNasser, Gina R. Maayah, Yaser Jararweh, Mostafa Z. Ali, Ghina’a Abu Deiab, Robert G. Reynolds, Talal Z. Ali, Ponnuthurai Nagaratnam Suganthan · 2025 · International Conference on Foundation and Large Language Models (FLLM)
17. HGCTBind: A hybrid architecture for predicting protein-DNA binding sites based on interpretable and contextual adaptive feature fusion
    Wentao Gong, Feifan Zhang, Junfan Chen, Kehan Lu · 2026 · Computational Biology and Chemistry
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19. Predicting protein-nucleic acid interactions via protein language models with biophysical and evolutionary priors
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20. TripleBind: a generalizable deep learning framework for protein-nucleic acid and protein-ligand binding sites prediction based on pre-trained protein language models
    Zhiwei Liu, Ruisheng Zhang · 2026 · Molecular Diversity
21. KANBind as a diagnostic probe for DNA-binding protein prediction: A prevalence-calibrated reality check under strict homology control
    QiPeng Wen, Shaohua Jiang, Yiwen Zhang · 2026 · Journal of Bioinformatics and Computational Biology
22. SGFormer: Simplifying and Scaling Graph Transformers With Single-Layer Attention and Approximation-Free Linear Complexity
    Qitian Wu, Kai Yang, Hengrui Zhang, David Wipf, Junchi Yan · 2026 · IEEE Transactions on Pattern Analysis and Machine Intelligence
23. A Novel AI Approach Utilizing Large Language Models and GWAS to Validate Drug Target Efficacy and Predict Adverse Effects
    Qingyi Zhu · 2026 · BIO Web of Conferences
24. Protein–nucleic acid binding site prediction using interpretable Kolmogorov–Arnold networks with hypergraph representation learning
    Yuefei Zhu, Guicong Sun, Weimin Zhu, Yongxian Fan, Zeheng Wu, Xianchen Zheng, Xiaoyong Pan · 2026 · Bioinformatics
25. Selection of Novel DNA Aptamers against HPV16 Biomarker, E6: An In Silico Approach
    Bonke Phathekile, Darius Riziki Martin, Nicole Remaliah Samantha Sibuyi, Abram Madimabe Madiehe, Martin Opiyo Onani, Mervin Meyer · 2026 · ACS Omega
26. RGTBind: RBF-gate graph transformer with spatially biased attention for protein–DNA binding-site prediction
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28. DNAreader: accurate prediction of DNA-binding residues in structured and disordered proteins using transformers and contrastive learning
    Jian Zhang, Sushmita Basu, Jingjing Qian, Lukasz Kurgan · 2026 · Nucleic Acids Research
29. Interpretable prediction of nucleic acid-binding proteins using a protein language model
    Hanjin Kim, Sung‐Gwon Lee, Jooseong Oh, Kee Kwang Kim, Eun‐Mi Kim, Chungoo Park · 2026 · Bioinformatics Advances
30. M2-PRNet: multi-scale and multi-modal learning for protein–RNA binding affinity prediction
    Junkai Wang, Gang Luo, Yunsong Yang, Zhilin Zhu, Min Li · 2026 · Bioinformatics
31. Addressing the Problems of Data Variations, Quality, and Scarcity in Training Deep Neural Networks
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32. DeepPANB: integrating protein language model with PaiNN equivariant graph neural networks for prediction of protein–nucleic acid binding sites
    Jilong Zhang, Zhixiang Wu, Jingjie Su, Xinyu Zhang, Yue Li, Zihan Li, Chunhua Li · 2026 · Briefings in Bioinformatics
33. DyProL: Dynamic Ensemble Representation Learning for Protein–Nucleic Acid Binding Site Prediction
    Pengpai Li, Yiman Liu, Liya Liang, Liu Rongming · 2026 · Advanced Science
34. AI and machine learning in structural biology
    Sanjay Kumar · 2026 · Elsevier eBooks
35. Interpretable Protein-Nucleic Acid Binding Site Prediction via Domain-Guided Multimodal Learning.
    Wen-Yu Xi, Ru-Heng Wang, Xiu-Cai Ye, Tetsuya Sakurai, Le-Yi Wei · 2026 · ACS Synthetic Biology
36. PNBind : Prediction of Nucleic Acid‐Binding Sites Using Protein Structure and Protein Language Models
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37. Intracellular complement Factor B couples inflammatory sensing to metabolism, chromatin regulation and maladaptive tissue repair
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