Template-based modeling of diverse protein interactions in CAPRI rounds 38-45

Proteins. 2020 Aug;88(8):939-947. doi: 10.1002/prot.25845. Epub 2019 Nov 21.


Structures of proteins complexed with other proteins, peptides, or ligands are essential for investigation of molecular mechanisms. However, the experimental structures of protein complexes of interest are often not available. Therefore, computational methods are widely used to predict these structures, and, of those methods, template-based modeling is the most successful. In the rounds 38-45 of the Critical Assessment of PRediction of Interactions (CAPRI), we applied template-based modeling for 9 of 11 protein-protein and protein-peptide interaction targets, resulting in medium and high-quality models for six targets. For the protein-oligosaccharide docking targets, we used constraints derived from template structures, and generated models of at least acceptable quality for most of the targets. Apparently, high flexibility of oligosaccharide molecules was the main cause preventing us from obtaining models of higher quality. We also participated in the CAPRI scoring challenge, the goal of which was to identify the highest quality models from a large pool of decoys. In this experiment, we tested VoroMQA, a scoring method based on interatomic contact areas. The results showed VoroMQA to be quite effective in scoring strongly binding and obligatory protein complexes, but less successful in the case of transient interactions. We extensively used manual intervention in both CAPRI modeling and scoring experiments. This oftentimes allowed us to select the correct templates from available alternatives and to limit the search space during the model scoring.

Keywords: docking; homology modeling; model quality assessment; protein-protein interactions; scoring; template-based modeling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Humans
  • Ligands
  • Molecular Docking Simulation*
  • Oligosaccharides / chemistry*
  • Oligosaccharides / metabolism
  • Peptides / chemistry*
  • Peptides / metabolism
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Protein Interaction Mapping
  • Proteins / chemistry*
  • Proteins / metabolism
  • Research Design
  • Software*
  • Structural Homology, Protein


  • Ligands
  • Oligosaccharides
  • Peptides
  • Proteins