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3DSwap - Knowledgebase of 3D Domain Swapping in Proteins:

3DSwap [3DSwap - Knowledgebase of 3D Domain Swapping in Proteins] is a comprehensive collection of protein structures that are reported to be involved in 3-Dimensional Domain Swapping. 3DSwap provides literature curated information and various structre related information about 3D Domain Swapping in Proteins. 3D domain swapping is a mechanism for two or more protein molecules to form a dimer or higher oligomer by exchanging an identical structural element (“domain”). It has been first reported in Diptheria Toxin [3DSwap Link] by Dr. Eisenberg et. al. 3DSwap provides detailed information various information about swapping, protein-protein interface, extent of swapping etc. Information related to domain swapping, residues involved in hinge region, residues involved in swapped regions etc. are extracted from orginal research publications after extensive literature curation.

Methodology:

PDB entries involved in 3Domain swapping were identified from literature and PDB using advanced search options. We have perfomed an initial filtering of entries by consulting DIAL Server, PDBSum. Final PDB entry list were used for literature curation. Publications related to individual PDB entries were curated for specific information related to domain swapping properties of individual entries. Structural Bioinformatics resources like RCSB PDB, PDB2GO, PDBSum, PQS, JOY, HERA, PyMol etc were used to annotate the individual entries in detail.

Database Contents:
3DSwap Database contents are divided in to following major categories:
  • LITERATURE CURATED INFORMATION
  • SEQUENCE
  • STRUCTURE
  • STRUCTURE FEATURES
  • DOWNLOADS

References:
  • Liu Y., Eisenberg D. 3D domain swapping: as domains continue to swap. Protein Sci. 2002;11:1285–1299.
    Mizuguchi K., Deane C.M., Blundell T.L., Johnson M.S., Overington J.P. JOY: protein sequence-structure representation and analysis. Bioinformatics. 1998;14:617–623.
  • Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402.
  • G. Pugalenthi, G. Archunan and R. Sowdhamini, DIAL: a web-based server for the automatic identification of structural domains in proteins. Nucleic Acids Res. 2005; 33(Web Server issue): W130–W132.
  • K. Shameer & R. Sowdhamini (2007) IWS: Integrated Web Server for protein sequence and structure analysis Bioinformation 2 (3): 86-90
3DSwap Database Team :

Prof. R. Sowdhamini (Contact : mini@ncbs.res.in)
K. Shameer