ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction
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Abstract
Predicting the functional sites of a protein from its structure, such as the binding sites of small molecules, other proteins or antibodies, sheds light on its function in vivo. Currently, two classes of methods prevail: machine learning models built on top of handcrafted features and comparative modeling. They are, respectively, limited by the expressivity of the handcrafted features and the availability of similar proteins. Here, we introduce ScanNet, an end-to-end, interpretable geometric deep learning model that learns features directly from 3D structures. ScanNet builds representations of atoms and amino acids based on the spatio-chemical arrangement of their neighbors. We train ScanNet for detecting protein-protein and protein-antibody binding sites, demonstrate its accuracy-including for unseen protein folds-and interpret the filters learned. Finally, we predict epitopes of the SARS-CoV-2 spike protein, validating known antigenic regions and predicting previously uncharacterized ones. Overall, ScanNet is a versatile, powerful and interpretable model suitable for functional site prediction tasks. A webserver for ScanNet is available from http://bioinfo3d.cs.tau.ac.il/ScanNet/ .
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Computational methods for binding site prediction on macromolecules
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Aligning large language models and geometric deep models for protein representation
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- Authors
- Tubiana, J., Schneidman-Duhovny, D., & Wolfson, H. J.
- Affiliations
- Tel Aviv University (IL)
- Corresponding author
- Tubiana, Jérôme
- Wolfson, Haim J.
- Venue
- Nature Methods
- Published
- 2022-05-30
- Volume
- 19
- Issue
- 6
- Pages
- 730-739
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W4229031603
- Cited by
- 274
- References
- 104
- Citations by year
- 2026: 70 · 2025: 75 · 2024: 69 · 2023: 48 · 2022: 11 · 2021: 1
- FWCI
- 16.82
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Human Frontier Science Program (LT001058/2019-C)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein binding site prediction, geometric deep learning, model interpretability, protein structure, protein-protein binding, epitope prediction, SARS-CoV-2 spike protein
- MeSH terms
- Deep Learning, COVID-19, SARS-CoV-2, Binding Sites, Humans, Protein Binding, Proteins, Spike Glycoprotein, Coronavirus
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