3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping
Shingate, Prashant N.
Manjunath, S. C. P.
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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.
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.
PublisherOxford University Press (OUP)
PubMed Central IDPMC3294423
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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.
- 3dswap-pred: prediction of 3D domain swapping from protein sequence using Random Forest approach.
- Authors: Shameer K, Pugalenthi G, Kandaswamy KK, Sowdhamini R
- Issue date: 2011 Oct
- Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome.
- Authors: Shameer K, Sowdhamini R
- Issue date: 2012 Apr 3
- 3D domain swapping: as domains continue to swap.
- Authors: Liu Y, Eisenberg D
- Issue date: 2002 Jun
- Three-dimensional domain swapping in the protein structure space.
- Authors: Huang Y, Cao H, Liu Z
- Issue date: 2012 Jun
- Analysis of domain-swapped oligomers reveals local sequence preferences and structural imprints at the linker regions and swapped interfaces.
- Authors: Shingate P, Sowdhamini R
- Issue date: 2012
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