Purpose of DSDBASE
The potential uses of DSDBASE are
Designing disulphide bonds in proteins. New features
Modelling peptides. New features
Designing disulphide bonds in proteinsThis disulphide database is useful to design site-directed mutants in order to enhance the thermal stability of the proteins in question.In this database disulphide bonds were designed in the stereochemicaly optimal region of the protein, so one can introduce a disulphide bond without straining the protein using this database.
This database provides information about all possible positions to introduce disulphide bonds in proteins along with there stereochemical grades. Option to get mutant file of interest and graphical view of mutant pdb also available
Present release considers PDB release, User can obtain disulphide bond information for above entries through the search archive provided on the top left corner of the menu frame.
To reach specific PDB entry, one can use following search options
1. Search by PDB code.
2. Search by Key word.
3. Search by Sequence.
Other than this, for new or missing entries option to run MODIP online also available
New features :
1. For enzymes, the active-site residues along with those within 50A distance to the active-site are highlighted. This can also be visualised through the Rasmol/Chime links provided.
2. For NMR determined PDB structures, all the models in the ensemble can be searched.
3. The co-ordinates and stereochemical parameters for all the possible positions for sulphur fixing are also provided.
4. Native disulphide bonds are marked differently.
The important application is to employ database for proposing three-dimentional models of disulphide-rich polypetides like toxins and small proteins.such small proteins are not rich in secondary structure and are stabilised by the covalent crosslinks.we have previously shown, for smaller dataset, that the present disulphide database could be successfully applied to modelling the N-terminal domain of hepatocyte growth factors (Donate et al., 1994)and the model was quite close the experimental structure (Chirgadze et al., 1998).
Picture: This picture shows the model of N-terminal domain of hepatocyte growth factors both proposed model and exprimental model.
For this application we have developed a non-redundant disulphide database, in order to avoid bias of data. User can probe the database for multipl disulphide bond system of particular connectivity, and get possible conformations for that region without any sequence information.
We have installed a search engine for Modelling disulphide rich peptides. This will get disulphide bond connectivity details from the user and search for the pattern in non-redundent database. Out put will be other proteins or peptides or sub-structural motif of a protein having simmilar connectivity pattern. Option for down loading the corrdinate files of the hits and graphical veiw are also available in output.
New features :
1. Now the user can also submit the sequence of the query peptide to get the sequence similarity with the substructural hits.
2. An option is provided on the search result page to filter the hits on the basis of user-defined sequence identity cut-off.
3. The predicted subcellular location of the query peptide is also provided.
4. Native disulphide bonds are highlighted.
5. Redox-active disulphide bonds are also highlighted.