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. 2023 Dec;91(12):1879-1888.
doi: 10.1002/prot.26554. Epub 2023 Jul 21.

VoroIF-GNN: Voronoi tessellation-derived protein-protein interface assessment using a graph neural network

Kliment Olechnovič  1 , Česlovas Venclovas  1
Affiliations

VoroIF-GNN: Voronoi tessellation-derived protein-protein interface assessment using a graph neural network

Kliment Olechnovič et al. Proteins. 2023 Dec.

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/.

Keywords: CASP; Voronoi tessellation; estimation of model accuracy; graph neural network; protein-protein complex; quality assessment.

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References

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