Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein-Peptide Complex Structures

Methods Mol Biol. 2020:2165:273-287. doi: 10.1007/978-1-0716-0708-4_16.

Abstract

Structural characterizations of protein-peptide complexes may require further improvements. These may include reconstruction of missing atoms and/or structure optimization leading to higher accuracy models. In this work, we describe a workflow that generates accurate structural models of peptide-protein complexes starting from protein-peptide models in C-alpha representation generated using CABS-dock molecular docking. First, protein-peptide models are reconstructed from their C-alpha traces to all-atom representation using MODELLER. Next, they are refined using Rosetta FlexPepDock. The described workflow allows for reliable all-atom reconstruction of CABS-dock models and their further improvement to high-resolution models.

Keywords: Coarse-grained model; Protein reconstruction; Protein refinement; Protein structure; Protein–peptide interaction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Molecular Docking Simulation / methods*
  • Peptides / chemistry*
  • Peptides / metabolism
  • Protein Binding
  • Protein Conformation*
  • Software
  • Workflow

Substances

  • Peptides