Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention
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Abstract
ABSTRACT Identifying and discovering druggable protein binding sites is an important early step in computer-aided drug discovery but remains a difficult task where most campaigns rely on a priori knowledge of binding sites from experiments. Here we present a novel binding site prediction method called Graph Attention Site Prediction (GrASP) and re-evaluate assumptions in nearly every step in the site prediction workflow from dataset preparation to model evaluation. GrASP is able to achieve state-of-the-art performance at recovering binding sites in PDB structures while maintaining a high degree of precision which will minimize wasted computation in downstream tasks such as docking and free energy perturbation.
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Cites
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- Authors
- Smith, Z., Strobel, M., Vani, B. P., & Tiwary, P.
- Affiliations
- University of Maryland, College Park (US)
- Corresponding author
- Tiwary, Pratyush
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2024-03-07
- Volume
- 64
- Issue
- 7
- Pages
- 2637-2644
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- PMC
- PMC11182664
- OpenAlex
- W4392626944
- Cited by
- 47
- References
- 6
- Citations by year
- 2026: 12 · 2025: 18 · 2024: 14 · 2023: 3
- FWCI
- 9.33
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- PubMed Central (submittedVersion, cc-by)
- Funders
- National Institute of General Medical Sciences (R35GM142719)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- protein binding site prediction, graph neural networks, attention mechanism, computational drug discovery, protein structure, PDB structures
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