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Structural Characterization of Protein–Protein Interactions with pyDockSAXS

Protocol
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 

Notes

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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© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Barcelona Supercomputing Center (BSC)BarcelonaSpain
  2. 2.Bijvoet Center for Biomolecular Research, Faculty of Science—ChemistryUtrecht UniversityUtrechtThe Netherlands
  3. 3.Centre de Biochimie Structurale, CNRS, INSERMUniversité de MontpellierMontpellierFrance
  4. 4.Institut de Biologia Molecular de Barcelona (IBMB)Consejo Superior de Investigaciones Científicas (CSIC)BarcelonaSpain
  5. 5.Instituto de Ciencias de la Vid y del Vino (ICVV)Consejo Superior de Investigaciones Científicas (CSIC)LogroñoSpain

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