3DSwap - Database of Domain Swapping in Proteins: Help Page
3DSwap is a comprehensive collection of protein structures that are reported to be involved in 3-Dimensional Domain Swapping. 3DSwap provides literature curated 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 were extracted from orginal research publications after extensive literature curation.
Terminology:
In 3DSwap we are frequently using the following terms to explain different feature of protein structures with 3D Domain swapping.
- Domain Swapping
- Domain-swapped Dimer
- Primary Interdomain Interface
- Secondary Interdomain Interface
- Secondary Minor Region
- Secondary Major Region
- Functional Unit (FU)
- Hinge Region
- Quasi-Domain Swapping
- Bonafide Domain Swapping
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 July 1; 33(Web Server issue): W130–W132.
3DSwap Database Team :
Prof. R. Sowdhamini (Contact : mini@ncbs.res.in)
K. Shameer
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