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Structural Characterization of Protein–Protein Interactions with pyDockSAXS

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Structural Bioinformatics

Part of the book series: Methods in Molecular Biology ((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.

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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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Authors and Affiliations

  1. Barcelona Supercomputing Center (BSC), Barcelona, Spain

    Brian Jiménez-García & Juan Fernández-Recio

  2. Bijvoet Center for Biomolecular Research, Faculty of Science—Chemistry, Utrecht University, Utrecht, The Netherlands

    Brian Jiménez-García

  3. Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France

    Pau Bernadó

  4. Institut de Biologia Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain

    Juan Fernández-Recio

  5. Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas (CSIC), Logroño, Spain

    Juan Fernández-Recio

Authors
  1. Brian Jiménez-García
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  2. Pau Bernadó
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  3. Juan Fernández-Recio
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Corresponding author

Correspondence to Juan Fernández-Recio .

Editor information

Editors and Affiliations

  1. Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary

    Zoltán Gáspári

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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

  • Print ISBN: 978-1-0716-0269-0

  • Online ISBN: 978-1-0716-0270-6

  • eBook Packages: Springer Protocols

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