Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction

Proteins. 2021 Dec;89(12):1834-1843. doi: 10.1002/prot.26167. Epub 2021 Jul 5.


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 our 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 intersubunit interfaces according to several accuracy measures. We attribute our relative success primarily to the emphasis on the interaction interface when modeling and scoring.

Keywords: PPI3D; VoroMQA; binding sites; docking; homology modeling; interface scoring; model quality assessment; protein complexes; protein-protein interactions; template-based modeling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Computational Biology
  • Models, Molecular*
  • Molecular Docking Simulation
  • Protein Conformation*
  • Protein Interaction Domains and Motifs
  • Proteins* / chemistry
  • Proteins* / metabolism
  • Sequence Analysis, Protein
  • Software*
  • Structural Homology, Protein*


  • Proteins