3DSwap+ | Semi-automated Knowledgebase of proteins involved in 3D domain swapping:
3DSwap+ [3DSwap+ - Semi-automated Knowledgebase of proteins involved in 3D domain swapping] is a semi-automated and 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 by using DIAL, an inhouse tool. Initial filtering of entries are performed by consulting DIAL
Server and PDBSum database and also manually curated. Final list of PDB entries were used for full length literature curation, if present. 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.
Liu Y., Eisenberg D. 3D domain swapping: as domains continue to swap. Protein Sci. 2002;11:1285-1299.
Khader Shameer, Prashant N. Shingate, Manjunath, S.C.P., Karthika, M., Ganesan Pugalenthi, Ramanathan Sowdhamini. 3DSwap: Curated Knowledgebase for proteins involved in 3D domain swapping. Database (2011) 2011.
Prashant Shingate and R. Sowdhamini. Analysis of domain swapped oligomers reveal local sequence preferences and structural imprints at the linker regions and swapped interfaces. PLoS One, 2012;7(7).
Prashant Shingate, Atul K. Upadhyay, U.S. Raghavender and R. Sowdhamini. (2012) Identification and Conformational Analysis of hinge regions in proteins that undergo domain swapping. To appear as a Chapter in a book entitled "Biomolecular Forms and Functions" (Eds. M. Bansal and N. Srinivasan) (in press).
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)
Prashant N Shingate, Atul K Upadhyay and Prof. R. Sowdhamini
