Source:Protein Structure Prediction, Springer US, New York, NY:273–287, 2020
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.