CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes

• Published in: Journal of molecular biology 2024-09, Vol.436 (17), p.168540, Article 168540
• Main Authors: Collins, Keeley W., Copeland, Matthew M., Brysbaert, Guillaume, Wodak, Shoshana J., Bonvin, Alexandre M.J.J., Kundrotas, Petras J., Vakser, Ilya A., Lensink, Marc F.
• Format: Article
• Language: English
• Subjects: Algorithms; blind prediction; CAPRI; Computational Biology - methods; Databases, Protein; Models, Molecular; Molecular Docking Simulation; Protein Binding; Protein Conformation; protein docking; Protein Interaction Mapping - methods; protein modeling; Proteins - chemistry; quality assessment; Software
• ISSN: 0022-2836; 1089-8638; 1089-8638
• DOI: 10.1016/j.jmb.2024.168540

[Display omitted] •CAPRI has catalyzed the development and defines the state of the art in the modeling of protein complexes.•DOCKGROUND is an established and regularly updated resource for protein complexes.•The CAPRI-Q resource applies the CAPRI assessment metrics to any number of submitted model structures and classifies them following CAPRI criteria.•The CAPRI-Q source code is freely available.•The CAPRI-Q web server is fully integrated into the DOCKGROUND resource. Protein interactions are essential for cellular processes. In recent years there has been significant progress in computational prediction of 3D structures of individual protein chains, with the best-performing algorithms reaching sub-Ångström accuracy. These techniques are now finding their way into the prediction of protein interactions, adding to the existing modeling approaches. The community-wide Critical Assessment of Predicted Interactions (CAPRI) has been a catalyst for the development of procedures for the structural modeling of protein assemblies by organizing blind prediction experiments. The predicted structures are assessed against unpublished experimentally determined structures using a set of metrics with proven robustness that have been established in the CAPRI community. In addition, several advanced benchmarking databases provide targets against which users can test docking and assembly modeling software. These include the Protein-Protein Docking Benchmark, the CAPRI Scoreset, and the Dockground database, all developed by members of the CAPRI community. Here we present CAPRI-Q, a stand-alone model quality assessment tool, which can be freely downloaded or used via a publicly available web server. This tool applies the CAPRI metrics to assess the quality of query structures against given target structures, along with other popular quality metrics such as DockQ, TM-score and l-DDT, and classifies the models according to the CAPRI model quality criteria. The tool can handle a variety of protein complex types including those involving peptides, nucleic acids, and oligosaccharides. The source code is freely available from https://gitlab.in2p3.fr/cmsb-public/CAPRI-Q and its web interface through the Dockground resource at https://dockground.compbio.ku.edu/assessment/.