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Structural Characterization of Protein–Protein Interactions with pyDockSAXS

Part of the Methods in Molecular Biology book series (MIMB,volume 2112)

Abstract

Structural characterization of protein–protein interactions can provide essential details to understand biological functions at the molecular level and to facilitate their manipulation for biotechnological and biomedical purposes. Unfortunately, the 3D structure is available for only a small fraction of all possible protein–protein interactions, due to the technical limitations of high-resolution structural determination methods. In this context, low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be combined with computational docking to provide structural models of protein–protein interactions at large scale. In this chapter, we describe the pyDockSAXS web server (https://life.bsc.es/pid/pydocksaxs), which uses pyDock docking and scoring to provide structural models that optimally satisfy the input SAXS data. This server, which is freely available to the scientific community, provides an automatic pipeline to model the structure of a protein–protein complex from SAXS data.

Key words

  • Protein–protein interactions
  • Structural modeling
  • Small-angle X-ray scattering (SAXS)
  • Computational docking
  • FTDock
  • CRYSOL
  • pyDock

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Acknowledgments

This work was supported by the Spanish Ministry of Science (grant BIO2016-79930-R), the European Union H2020 programme (grant MuG 676566), and the Labex EpiGenMed, an “Investissements d’avenir” program (ANR-10-LABX-12-01). The CBS is a member of France-BioImaging (FBI) and the French Infrastructure for Integrated Structural Biology (FRISBI), two national infrastructures supported by the French National Research Agency (ANR-10-INSB-04-01 and ANR-10-INSB-05, respectively).

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Correspondence to Juan Fernández-Recio .

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Jiménez-García, B., Bernadó, P., Fernández-Recio, J. (2020). Structural Characterization of Protein–Protein Interactions with pyDockSAXS. In: Gáspári, Z. (eds) Structural Bioinformatics. Methods in Molecular Biology, vol 2112. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0270-6_10

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  • DOI: https://doi.org/10.1007/978-1-0716-0270-6_10

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  • Publisher Name: Humana, New York, NY

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