ScanNet: A Web Server for Structure-based Prediction of Protein Binding Sites with Geometric Deep Learning |
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| Institution: | 1. Blavatnik School of Computer Science, Tel Aviv University, Israel;2. School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel;1. Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO, USA;2. Department of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA;3. Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA;4. Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA;1. Department of Chemistry Imperial College London, United Kingdom;2. Department of Mathematics, Imperial College London, United Kingdom;1. Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix 138671, Singapore;2. Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore |
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| Abstract: | Predicting the various binding sites of a protein from its structure sheds light on its function and paves the way towards design of interaction inhibitors. Here, we report ScanNet, a freely available web server for prediction of protein–protein, protein - disordered protein and protein - antibody binding sites from structure. ScanNet (Spatio-Chemical Arrangement of Neighbors Network) is an end-to-end, interpretable geometric deep learning model that learns spatio-chemical patterns directly from 3D structures. ScanNet consistently outperforms Machine Learning models based on handcrafted features and comparative modeling approaches. The web server is linked to both the PDB and AlphaFoldDB, and supports user-provided structure files. Predictions can be readily visualized on the website via the Molstar web app and locally via ChimeraX. ScanNet is available at http://bioinfo3d.cs.tau.ac.il/ScanNet/. |
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