Protocols for all-atom reconstruction and high-resolution refinement of protein-peptide complex structures
Badaczewska-Dawid, A.; Khramushin, A.; Kolinski, A.; Schueler-Furman, O.; Kmiecik, S.
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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 RosettaFlexPepDock. The described workflow allows for reliable all-atom reconstruction of CABS-dock models and their further improvement to high-resolution models.
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