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Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction
  • Justas Dapkunas,
  • Kliment Olechnovič,
  • Česlovas Venclovas
Justas Dapkunas
Vilnius University
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Kliment Olechnovič
Villnius University
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Česlovas Venclovas
Villnius University
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Abstract

The goal of CASP experiments is to monitor the progress in the protein structure prediction field. During the 14th CASP edition we aimed to test our capabilities of predicting structures of protein complexes. Our protocol for modeling protein assemblies included both template-based modeling and free docking. Structural templates were identified using sensitive sequence-based searches. If sequence-based searches failed, we performed structure-based template searches using selected CASP server models. In the absence of reliable templates we applied free docking starting from monomers generated by CASP servers. We evaluated and ranked models of protein complexes using an improved version of protein structure quality assessment method, VoroMQA, taking into account both interaction interface and global structure scores. If reliable templates could be identified, generally accurate models of protein assemblies were generated with the exception of an antibody-antigen interaction. The success of free docking mainly depended on the accuracy of initial subunit models and on the scoring of docking solutions. To put our overall results in perspective, we analyzed our performance in the context of other CASP groups. Although the subunits in our assembly models often were not of the top quality, these models had, overall, the best predicted interfaces according to several protein-protein interface accuracy measures. Since we did not use co-evolution-based prediction of inter-chain contacts, we attribute our relative success in predicting interfaces primarily to the emphasis on the interaction interface when modeling and scoring.

Peer review status:UNDER REVIEW

01 May 2021Submitted to PROTEINS: Structure, Function, and Bioinformatics
03 May 2021Submission Checks Completed
03 May 2021Assigned to Editor
03 May 2021Reviewer(s) Assigned
18 May 2021Review(s) Completed, Editorial Evaluation Pending
19 May 2021Editorial Decision: Revise Minor
31 May 20211st Revision Received
02 Jun 2021Submission Checks Completed
02 Jun 2021Assigned to Editor
02 Jun 2021Reviewer(s) Assigned
16 Jun 2021Review(s) Completed, Editorial Evaluation Pending
17 Jun 2021Editorial Decision: Revise Minor
21 Jun 20212nd Revision Received
23 Jun 2021Submission Checks Completed
23 Jun 2021Assigned to Editor
23 Jun 2021Review(s) Completed, Editorial Evaluation Pending