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3DSwap

A curated knowledegbase of protein structures that are reported to be involved in 3-Dimensional Domain Swapping. 3DSwap provides literature curated information and various structure related information about 3D Domain Swapping in Proteins. 3DSwap provides detailed various information about swapping, hinge region, swapped region, extent of swapping etc. Information related to domain swapping, residues involved in hinge region, residues involved in swapped regions etc. are extracted from original research publications after extensive literature curation.

URL: http://caps.ncbs.res.in/3dswap/index.html

Resource ID: nlx_143564     Resource Type: Resource     Version: Latest Version

Keywords

protein structure, protein, structure, 3d domain swapping, function, sequence, domain swap, 3d spatial image

Abbreviation

3DSwap

Synonyms

3DSwap - Knowledgebase of proteins involved in 3D domain swapping, 3DSwap: Knowledgebase of 3D Domain Swapping in Proteins, 3D Swap, 3DSwap Database

Funding Information

Tata Institute of Fundamental Research; Mumbai; India, National Centre for Biological Sciences, Wellcome Trust,

Additional Resource Types

Database

Supercategory

Resource

Parent Organization

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am October 3, 2011

Originated From

SciCrunch

Changes from Previous Version

  • Funding Information was changed
  • Additional Resource Types was changed

Version 2

Created 2 weeks ago by Christie Wang

Version 1

Created 4 years ago by Anonymous

3DSwap: curated knowledgebase of proteins involved in 3D domain swapping.

  • Shameer K
  • Database (Oxford)
  • 2011 30

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.

3dswap-pred: prediction of 3D domain swapping from protein sequence using Random Forest approach.

  • Shameer K
  • Protein Pept. Lett.
  • 2011 31

3D domain swapping is a protein structural phenomenon that mediates the formation of the higher order oligomers in a variety of proteins with different structural and functional properties. 3D domain swapping is associated with a variety of biological functions ranging from oligomerization to pathological conformational diseases. 3D domain swapping is realised subsequent to structure determination where the protein is observed in the swapped conformation in the oligomeric state. This is a limiting step to understand this important structural phenomenon in a large scale from the growing sequence data. A new machine learning approach, 3dswap-pred, has been developed for the prediction of 3D domain swapping in protein structures from mere sequence data using the Random Forest approach. 3Dswap-pred is implemented using a positive sequence dataset derived from literature based structural curation of 297 structures. A negative sequence dataset is obtained from 462 SCOP domains using a new sequence data mining approach and a set of 126 sequencederived features. Statistical validation using an independent dataset of 68 positive sequences and 313 negative sequences revealed that 3dswap-pred achieved an accuracy of 63.8%. A webserver is also implemented using the 3dswap-pred Random Forest model. The server is available from the URL: http://caps.ncbs.res.in/3dswap-pred.