3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping

Handle URI:
http://hdl.handle.net/10754/325442
Title:
3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping
Authors:
Shameer, Khader; Shingate, Prashant N.; Manjunath, S. C. P.; Karthika, M.; Pugalenthi, Ganesan; Sowdhamini, Ramanathan
Abstract:
Three-dimensional domain swapping is a unique protein structural phenomenon where two or more protein chains in a protein oligomer share a common structural segment between individual chains. This phenomenon is observed in an array of protein structures in oligomeric conformation. Protein structures in swapped conformations perform diverse functional roles and are also associated with deposition diseases in humans. We have performed in-depth literature curation and structural bioinformatics analyses to develop an integrated knowledgebase of proteins involved in 3D domain swapping. The hallmark of 3D domain swapping is the presence of distinct structural segments such as the hinge and swapped regions. We have curated the literature to delineate the boundaries of these regions. In addition, we have defined several new concepts like 'secondary major interface' to represent the interface properties arising as a result of 3D domain swapping, and a new quantitative measure for the 'extent of swapping' in structures. The catalog of proteins reported in 3DSwap knowledgebase has been generated using an integrated structural bioinformatics workflow of database searches, literature curation, by structure visualization and sequence-structure-function analyses. The current version of the 3DSwap knowledgebase reports 293 protein structures, the analysis of such a compendium of protein structures will further the understanding molecular factors driving 3D domain swapping. The Author(s) 2011.
KAUST Department:
Biosciences Core Lab; Structural and Functional Bioinformatics Group
Citation:
Shameer K, Shingate PN, Manjunath SCP, Karthika M, Pugalenthi G, et al. (2011) 3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. Database 2011: bar042-bar042. doi:10.1093/database/bar042.
Publisher:
Oxford University Press
Journal:
Database
Issue Date:
29-Sep-2011
DOI:
10.1093/database/bar042
PubMed ID:
21959866
PubMed Central ID:
PMC3294423
Type:
Article
ISSN:
17580463
Appears in Collections:
Articles; Biosciences Core Lab; Structural and Functional Bioinformatics Group

Full metadata record

DC FieldValue Language
dc.contributor.authorShameer, Khaderen
dc.contributor.authorShingate, Prashant N.en
dc.contributor.authorManjunath, S. C. P.en
dc.contributor.authorKarthika, M.en
dc.contributor.authorPugalenthi, Ganesanen
dc.contributor.authorSowdhamini, Ramanathanen
dc.date.accessioned2014-08-27T09:51:30Z-
dc.date.available2014-08-27T09:51:30Z-
dc.date.issued2011-09-29en
dc.identifier.citationShameer K, Shingate PN, Manjunath SCP, Karthika M, Pugalenthi G, et al. (2011) 3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. Database 2011: bar042-bar042. doi:10.1093/database/bar042.en
dc.identifier.issn17580463en
dc.identifier.pmid21959866en
dc.identifier.doi10.1093/database/bar042en
dc.identifier.urihttp://hdl.handle.net/10754/325442en
dc.description.abstractThree-dimensional domain swapping is a unique protein structural phenomenon where two or more protein chains in a protein oligomer share a common structural segment between individual chains. This phenomenon is observed in an array of protein structures in oligomeric conformation. Protein structures in swapped conformations perform diverse functional roles and are also associated with deposition diseases in humans. We have performed in-depth literature curation and structural bioinformatics analyses to develop an integrated knowledgebase of proteins involved in 3D domain swapping. The hallmark of 3D domain swapping is the presence of distinct structural segments such as the hinge and swapped regions. We have curated the literature to delineate the boundaries of these regions. In addition, we have defined several new concepts like 'secondary major interface' to represent the interface properties arising as a result of 3D domain swapping, and a new quantitative measure for the 'extent of swapping' in structures. The catalog of proteins reported in 3DSwap knowledgebase has been generated using an integrated structural bioinformatics workflow of database searches, literature curation, by structure visualization and sequence-structure-function analyses. The current version of the 3DSwap knowledgebase reports 293 protein structures, the analysis of such a compendium of protein structures will further the understanding molecular factors driving 3D domain swapping. The Author(s) 2011.en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.rightsThis is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.5en
dc.subjectproteinen
dc.subjectbiologyen
dc.subjectcattleen
dc.subjectchemical structureen
dc.subjectchemistryen
dc.subjectcomputer interfaceen
dc.subjectdata baseen
dc.subjectmethodologyen
dc.subjectmolecular geneticsen
dc.subjectprotein conformationen
dc.subjectprotein databaseen
dc.subjectprotein tertiary structureen
dc.subjectCattleen
dc.subjectComputational Biologyen
dc.subjectDatabase Management Systemsen
dc.subjectDatabases, Proteinen
dc.subjectModels, Molecularen
dc.subjectMolecular Sequence Annotationen
dc.subjectProtein Conformationen
dc.subjectProtein Structure, Tertiaryen
dc.subjectProteinsen
dc.subjectUser-Computer Interfaceen
dc.title3DSwap: Curated knowledgebase of proteins involved in 3D domain swappingen
dc.typeArticleen
dc.contributor.departmentBiosciences Core Laben
dc.contributor.departmentStructural and Functional Bioinformatics Groupen
dc.identifier.journalDatabaseen
dc.identifier.pmcidPMC3294423en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionNational Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka 560065, Indiaen
dc.contributor.institutionDepartment of Molecular Medicine, Manipal University, Manipal, Karnataka 576104, Indiaen
dc.contributor.institutionDepartment of Biotechnology, SASTRA University, Tanjore, Tamil Nadu 613401, Indiaen
dc.contributor.institutionDivision of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, United Statesen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorGanesan, Pugalenthien
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