VoroIF‐GNN : Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network
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Abstract
We present VoroIF‐GNN (Voronoi InterFace Graph Neural Network), a novel method for assessing inter‐subunit interfaces in a structural model of a protein–protein complex, relying solely on the input structure without any additional information. Given a multimeric protein structural model, we derive interface contacts from the Voronoi tessellation of atomic balls, construct a graph of those contacts, and predict the accuracy of every contact using an attention‐based GNN. The contact‐level predictions are then summarized to produce whole interface‐level scores. VoroIF‐GNN was blindly tested for its ability to estimate the accuracy of protein complexes during CASP15 and showed strong performance in selecting the best multimeric model out of many. The method implementation is freely available at https://kliment-olechnovic.github.io/voronota/expansion_js/ .
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References 33 · Cited by 38
- Authors
- Olechnovič, K., & Venclovas, Č.
- Affiliations
- Vilnius University (LT)
- Corresponding author
- Olechnovič, Kliment
- Venclovas, Česlovas
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2023-07-21
- Volume
- 91
- Issue
- 12
- Pages
- 1879-1888
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W4385075189
- Cited by
- 38
- References
- 33
- Citations by year
- 2026: 11 · 2025: 16 · 2024: 7 · 2023: 4
- FWCI
- 3.39
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- Funders
- Lietuvos Mokslo Taryba (S‐MIP‐21‐35)
- 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 › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- protein-protein interfaces, Voronoi tessellation, graph neural networks, multimeric proteins, model selection
- MeSH terms
- Models, Molecular, Proteins, Neural Networks, Computer
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