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dc.contributor.authorShameer, Khader
dc.contributor.authorShingate, Prashant N.
dc.contributor.authorManjunath, S. C. P.
dc.contributor.authorKarthika, M.
dc.contributor.authorGanesan, Pugalenthi
dc.contributor.authorSowdhamini, Ramanathan
dc.date.accessioned2014-08-27T09:51:30Z
dc.date.available2014-08-27T09:51:30Z
dc.date.issued2011-09-29
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.
dc.identifier.issn17580463
dc.identifier.pmid21959866
dc.identifier.doi10.1093/database/bar042
dc.identifier.urihttp://hdl.handle.net/10754/325442
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.
dc.language.isoen
dc.publisherOxford University Press (OUP)
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.
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.5
dc.subjectprotein
dc.subjectbiology
dc.subjectcattle
dc.subjectchemical structure
dc.subjectchemistry
dc.subjectcomputer interface
dc.subjectdata base
dc.subjectmethodology
dc.subjectmolecular genetics
dc.subjectprotein conformation
dc.subjectprotein database
dc.subjectprotein tertiary structure
dc.subjectCattle
dc.subjectComputational Biology
dc.subjectDatabase Management Systems
dc.subjectDatabases, Protein
dc.subjectModels, Molecular
dc.subjectMolecular Sequence Annotation
dc.subjectProtein Conformation
dc.subjectProtein Structure, Tertiary
dc.subjectProteins
dc.subjectUser-Computer Interface
dc.title3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping
dc.typeArticle
dc.contributor.departmentBioscience Core Lab
dc.contributor.departmentStructural and Functional Bioinformatics Group
dc.identifier.journalDatabase
dc.identifier.pmcidPMC3294423
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionNational Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka 560065, India
dc.contributor.institutionDepartment of Molecular Medicine, Manipal University, Manipal, Karnataka 576104, India
dc.contributor.institutionDepartment of Biotechnology, SASTRA University, Tanjore, Tamil Nadu 613401, India
dc.contributor.institutionDivision of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, United States
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personGanesan, Pugalenthi
refterms.dateFOA2018-06-14T04:31:43Z
dc.date.published-online2011-09-29
dc.date.published-print2011-09-29


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This 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.
Except where otherwise noted, this item's license is described as This 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.