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Nucleic Acids Research, 2004, Vol. 32, Database issue D200-D202
© 2004 Oxford University Press

DSDBASE: a consortium of native and modelled disulphide bonds in proteins

A. Vinayagam1, G. Pugalenthi1, R. Rajesh and R. Sowdhamini*

National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560065, India

*To whom correspondence should be addressed. Tel: +91 80 3636421; Fax: +91 80 3636462; Email: mini{at}ncbs.res.in
Present address:
A. Vinayagam, Department of Molecular Biophysics, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

DSDBASE is a database of disulphide bonds in proteins, which provides information on native disulphides and those that are stereochemically possible between pairs of residues for all known protein structural entries. The modelling of disulphides has been performed, using MODIP, by the identification of residue pairs that can strainlessly accommodate a covalent cross-link. We also assess the stereochemical quality of the covalent cross-link and grade them appropriately. One of the potential uses of the database is to design site-directed mutants in order to enhance the thermal stability of a protein. The proposed sites of mutations can be viewed specifically with respect to active sites of enzymes and across physiological dimers. The occurrence of native and modelled disulphides increases the dimensions of the database enormously. This database can also be employed for proposing three-dimensional models of disulphide-rich short polypeptides. The database can be accessed from http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html. Supplementary information can be accessed from http://www.ncbs.res.in/ ~faculty/mini/dsdbase/nar/suppl.htm.


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