دورية أكاديمية
PGBind: pocket-guided explicit attention learning for protein-ligand docking.
| العنوان: | PGBind: pocket-guided explicit attention learning for protein-ligand docking. |
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| المؤلفون: | Shen A; Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, 131 Dong'an Road, Shanghai 200032, China.; Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University, 131 Dong'an Road, Shanghai 200032, China., Yuan M; Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, 131 Dong'an Road, Shanghai 200032, China.; Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University, 131 Dong'an Road, Shanghai 200032, China., Ma Y; Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, 131 Dong'an Road, Shanghai 200032, China.; Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University, 131 Dong'an Road, Shanghai 200032, China., Du J; Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, 131 Dong'an Road, Shanghai 200032, China.; Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University, 131 Dong'an Road, Shanghai 200032, China., Wang M; Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, 131 Dong'an Road, Shanghai 200032, China.; Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University, 131 Dong'an Road, Shanghai 200032, China. |
| المصدر: | Briefings in bioinformatics [Brief Bioinform] 2024 Jul 25; Vol. 25 (5). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: Oxford : Oxford University Press Original Publication: London ; Birmingham, AL : H. Stewart Publications, [2000- |
| مواضيع طبية MeSH: | Ligands* , Proteins*/chemistry , Proteins*/metabolism , Drug Discovery*, Algorithms ; Binding Sites ; Computational Biology/methods ; Deep Learning ; Molecular Docking Simulation ; Protein Binding ; Protein Conformation |
| مستخلص: | As more and more protein structures are discovered, blind protein-ligand docking will play an important role in drug discovery because it can predict protein-ligand complex conformation without pocket information on the target proteins. Recently, deep learning-based methods have made significant advancements in blind protein-ligand docking, but their protein features are suboptimal because they do not fully consider the difference between potential pocket regions and non-pocket regions in protein feature extraction. In this work, we propose a pocket-guided strategy for guiding the ligand to dock to potential docking regions on a protein. To this end, we design a plug-and-play module to enhance the protein features, which can be directly incorporated into existing deep learning-based blind docking methods. The proposed module first estimates potential pocket regions on the target protein and then leverages a pocket-guided attention mechanism to enhance the protein features. Experiments are conducted on integrating our method with EquiBind and FABind, and the results show that their blind-docking performances are both significantly improved and new start-of-the-art performance is achieved by integration with FABind. (© The Author(s) 2024. Published by Oxford University Press.) |
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| معلومات مُعتمدة: | 23S41900400 Science and Technology Innovation Plan Of Shanghai Science and Technology Commission; FD-AI4S04183 Fudan University Science Intelligence Special Fund |
| فهرسة مساهمة: | Keywords: AI for science; drug discovery; protein–ligand blind docking; protein–ligand docking |
| المشرفين على المادة: | 0 (Ligands) 0 (Proteins) |
| تواريخ الأحداث: | Date Created: 20240918 Date Completed: 20240918 Latest Revision: 20240925 |
| رمز التحديث: | 20240925 |
| مُعرف محوري في PubMed: | PMC11410380 |
| DOI: | 10.1093/bib/bbae455 |
| PMID: | 39293803 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1477-4054 |
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| DOI: | 10.1093/bib/bbae455 |