Benchmarking of structure refinement methods for protein complex models

Proteins. 2022 Jan;90(1):83-95. doi: 10.1002/prot.26188. Epub 2021 Aug 3.


Protein structure docking is the process in which the quaternary structure of a protein complex is predicted from individual tertiary structures of the protein subunits. Protein docking is typically performed in two main steps. The subunits are first docked while keeping them rigid to form the complex, which is then followed by structure refinement. Structure refinement is crucial for a practical use of computational protein docking models, as it is aimed for correcting conformations of interacting residues and atoms at the interface. Here, we benchmarked the performance of eight existing protein structure refinement methods in refinement of protein complex models. We show that the fraction of native contacts between subunits is by far the most straightforward metric to improve. However, backbone dependent metrics, based on the Root Mean Square Deviation proved more difficult to improve via refinement.

Keywords: CAPRI; protein complexes; protein docking; protein structure refinement; protein-protein interaction.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Benchmarking
  • Computational Biology / methods*
  • Databases, Protein
  • Molecular Docking Simulation / methods*
  • Protein Conformation*
  • Proteins / chemistry*
  • Proteins / genetics
  • Proteins / metabolism


  • Proteins