Structural Characterization of Protein–Protein Interactions with pyDockSAXS
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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Format: | capítulo de libro biblioteca |
Language: | English |
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Springer Nature
2020
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Subjects: | Protein–protein interactions, Structural modeling, Small-angle X-ray scattering (SAXS), Computational docking, FTDock, CRYSOL, pyDock, |
Online Access: | http://hdl.handle.net/10261/232368 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100001665 |
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dig-icvv-es-10261-2323682021-03-06T05:56:19Z Structural Characterization of Protein–Protein Interactions with pyDockSAXS Jiménez-García, Brian Bernadó, Pau Fernández-Recio, Juan Ministerio de Economía y Competitividad (España) European Commission Labex EpiGenMed Agence Nationale de la Recherche (France) Protein–protein interactions Structural modeling Small-angle X-ray scattering (SAXS) Computational docking FTDock CRYSOL pyDock 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. 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). Peer reviewed 2021-03-03T10:27:26Z 2021-03-03T10:27:26Z 2020 capítulo de libro http://purl.org/coar/resource_type/c_3248 Structural Bioinformatics 131-144 (2020) 978-1-0716-0269-0 http://hdl.handle.net/10261/232368 10.1007/978-1-0716-0270-6_10 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100001665 en #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2016-79930-R info:eu-repo/grantAgreement/EC/H2020/676566 Methods in Molecular Biology 2112 https://doi.org/10.1007/978-1-0716-0270-6_10 Sí none Springer Nature |
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Protein–protein interactions Structural modeling Small-angle X-ray scattering (SAXS) Computational docking FTDock CRYSOL pyDock Protein–protein interactions Structural modeling Small-angle X-ray scattering (SAXS) Computational docking FTDock CRYSOL pyDock |
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Protein–protein interactions Structural modeling Small-angle X-ray scattering (SAXS) Computational docking FTDock CRYSOL pyDock Protein–protein interactions Structural modeling Small-angle X-ray scattering (SAXS) Computational docking FTDock CRYSOL pyDock Jiménez-García, Brian Bernadó, Pau Fernández-Recio, Juan Structural Characterization of Protein–Protein Interactions with pyDockSAXS |
description |
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. |
author2 |
Ministerio de Economía y Competitividad (España) |
author_facet |
Ministerio de Economía y Competitividad (España) Jiménez-García, Brian Bernadó, Pau Fernández-Recio, Juan |
format |
capítulo de libro |
topic_facet |
Protein–protein interactions Structural modeling Small-angle X-ray scattering (SAXS) Computational docking FTDock CRYSOL pyDock |
author |
Jiménez-García, Brian Bernadó, Pau Fernández-Recio, Juan |
author_sort |
Jiménez-García, Brian |
title |
Structural Characterization of Protein–Protein Interactions with pyDockSAXS |
title_short |
Structural Characterization of Protein–Protein Interactions with pyDockSAXS |
title_full |
Structural Characterization of Protein–Protein Interactions with pyDockSAXS |
title_fullStr |
Structural Characterization of Protein–Protein Interactions with pyDockSAXS |
title_full_unstemmed |
Structural Characterization of Protein–Protein Interactions with pyDockSAXS |
title_sort |
structural characterization of protein–protein interactions with pydocksaxs |
publisher |
Springer Nature |
publishDate |
2020 |
url |
http://hdl.handle.net/10261/232368 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100001665 |
work_keys_str_mv |
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