The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses

Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva
BMC Bioinformatics, (2020)

Keywords

Ranking, Docking models, Docking decoys, Prediction, Interface analysis, Consensus, Performance, Clust-CONSRANK, COCOMAPS

Abstract

​Properly scoring protein-protein docking models to single out the correct ones is an open challenge, also object of assessment in CAPRI (Critical Assessment of PRedicted Interactions), a community-wide blind docking experiment. We introduced in the field CONSRANK (CONSensus RANKing), the first pure consensus method. Also available as a web server, CONSRANK ranks docking models in an ensemble based on their ability to match the most frequent inter-residue contacts in it. We have been blindly testing CONSRANK in all the latest CAPRI rounds, where we showed it to perform competitively with the state-of-the-art energy and knowledge-based scoring functions. More recently, we developed Clust-CONSRANK, an algorithm introducing a contact-based clustering of the models as a preliminary step of the CONSRANK scoring process.

In the latest CASP13-CAPRI joint experiment, we participated as scorers with a novel pipeline, combining both our scoring tools, CONSRANK and Clust-CONSRANK, with our interface analysis tool COCOMAPS. Selection of the 10 models for submission was guided by the strength of the emerging consensus, and their final ranking was assisted by results of the interface analysis.

Code

https://doi.org/10.1186/s12859-020-03600-8

Sources

Website PDF