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bioRxiv · 10.1101/692160

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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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 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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Badaczewska-Dawid, A., Khramushin, A., Kolinski, A., Schueler-Furman, O., Kmiecik, S.. 2019-07-05. Protocols for all-atom reconstruction and high-resolution refinement of protein-peptide complex structures. https://doi.org/10.1101/692160

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