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.
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Acknowledgments
A.E.B-D, A.Ko., and S.K. received funding from NCN Poland, Grant MAESTRO2014/14/A/ST6/00088. O.S-F. and A.Kh. received funding from the ISF, Grant 717/17.
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Badaczewska-Dawid, A.E., Khramushin, A., Kolinski, A., Schueler-Furman, O., Kmiecik, S. (2020). Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 2165. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0708-4_16
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DOI: https://doi.org/10.1007/978-1-0716-0708-4_16
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