Prediction of Biomolecular Complexes

Handle URI:
http://hdl.handle.net/10754/623894
Title:
Prediction of Biomolecular Complexes
Authors:
Vangone, Anna; Oliva, Romina; Cavallo, Luigi ( 0000-0002-1398-338X ) ; Bonvin, Alexandre M. J. J.
Abstract:
Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.
KAUST Department:
KAUST Catalysis Center (KCC); Physical Sciences and Engineering (PSE) Division
Citation:
Vangone A, Oliva R, Cavallo L, Bonvin AMJJ (2017) Prediction of Biomolecular Complexes. From Protein Structure to Function with Bioinformatics: 265–292. Available: http://dx.doi.org/10.1007/978-94-024-1069-3_8.
Publisher:
Springer Netherlands
Journal:
From Protein Structure to Function with Bioinformatics
Issue Date:
12-Apr-2017
DOI:
10.1007/978-94-024-1069-3_8
Type:
Book Chapter
Sponsors:
AV was supported by Marie Skłodowska-Curie Individual Fellowship H2020 MSCA-IF-2015 [BAP-659025]. RO was supported by Regione Campania [LR5-AF2008].
Additional Links:
http://link.springer.com/chapter/10.1007/978-94-024-1069-3_8
Appears in Collections:
Physical Sciences and Engineering (PSE) Division; KAUST Catalysis Center (KCC); Book Chapters

Full metadata record

DC FieldValue Language
dc.contributor.authorVangone, Annaen
dc.contributor.authorOliva, Rominaen
dc.contributor.authorCavallo, Luigien
dc.contributor.authorBonvin, Alexandre M. J. J.en
dc.date.accessioned2017-05-31T11:23:12Z-
dc.date.available2017-05-31T11:23:12Z-
dc.date.issued2017-04-12en
dc.identifier.citationVangone A, Oliva R, Cavallo L, Bonvin AMJJ (2017) Prediction of Biomolecular Complexes. From Protein Structure to Function with Bioinformatics: 265–292. Available: http://dx.doi.org/10.1007/978-94-024-1069-3_8.en
dc.identifier.doi10.1007/978-94-024-1069-3_8en
dc.identifier.urihttp://hdl.handle.net/10754/623894-
dc.description.abstractAlmost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.en
dc.description.sponsorshipAV was supported by Marie Skłodowska-Curie Individual Fellowship H2020 MSCA-IF-2015 [BAP-659025]. RO was supported by Regione Campania [LR5-AF2008].en
dc.publisherSpringer Netherlandsen
dc.relation.urlhttp://link.springer.com/chapter/10.1007/978-94-024-1069-3_8en
dc.subjectProtein-protein complexesen
dc.subjectProtein-peptide complexesen
dc.subjectDockingen
dc.subjectSearchingen
dc.subjectScoringen
dc.subjectData-driven dockingen
dc.subjectHADDOCKen
dc.subjectCAPRIen
dc.subjectFlexibilityen
dc.subjectBinding affinityen
dc.subjectPRODIGYen
dc.subjectCONSRANKen
dc.titlePrediction of Biomolecular Complexesen
dc.typeBook Chapteren
dc.contributor.departmentKAUST Catalysis Center (KCC)en
dc.contributor.departmentPhysical Sciences and Engineering (PSE) Divisionen
dc.identifier.journalFrom Protein Structure to Function with Bioinformaticsen
dc.contributor.institutionComputational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science—Chemistry, Utrecht University, 3584, Utrecht, The Netherlandsen
dc.contributor.institutionDepartment of Sciences and Technologies, University “Parthenope” of Naples, Centro Direzionale Isola C4, 80143, Naples, Italyen
kaust.authorCavallo, Luigien
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