3DSwap | Knowledgebase of proteins involved in 3D domain swapping

3DSwap | Knowledgebase of proteins involved in 3D domain swapping:

3DSwap [3DSwap - Knowledgebase of proteins involved in 3D domain swapping] is 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. 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 [ 1DDT in 3DSwap Knowledgebase]. 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 orginal research publications after extensive literature curation.

Methodology:

3DSwap is a novel structural bioinformatics resource that provides the curated information and various sequence and structural features about the proteins involved in 3D domain swaping phenomenon. PDB entries involved in 3D Domain swapping were identified from integrated literature search and searches in PDB using advanced search options. Initial filtering of entries are performed by consulting DIAL Server and PDBSum database. Final list of PDB entries were used for full length literature curation. Publications related to individual PDB entries were curated for specific information related to domain swapping (hinge region, swapped region and other sequence and structural features). Structural Bioinformatics resources like RCSB PDB, SIFTS, PDBSum, PDBe, JOY, PyMol and databases like SCOP and Pfam were used to annotate the individual entries in great detail.

Database Contents:
3DSwap Database contents are divided in to following major categories: Literature Curated information, Visualization, Sequence features, Structure Features, Function annotation and Download.
3DSwap : Database Statistics:

3DSwap : Database Statistics as on December 2010 Total number of protein structures with curated information reported in 3DSwap : 293

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

K. Shameer, G. Pugalenthi, K. Kandaswamy, P. N. Suganthan, G. Archunan and R. Sowdhamini (2010). Insights into protein sequence and structure-derived features mediating 3D domain swapping mechanism using support vector machine based approach. Bioinformatics and Biology Insights 2010:4 1-10

3DSwap Database Team :
Prof. R. Sowdhamini (Contact : mini@ncbs.res.in)
Khader Shameer, Prashant N Shingate, Manjunath SCP, Karthika M. G, Ganesan Pugalenthi and Prof. R. Sowdhamini