Database to extract all human proteins having disulphide bonds from pdb, uniprot or others

Question

[Rm]

CMD database (currently not working); DSDbase (2003 version)

Any other suggestions?

Answer 1

[Siva]

Have you considered getting the information directly from PDB?

You can do a PDB advanced search by setting the Source Organism to Homo sapiens and using the Number of Disulfide Bonds between 1 and however many you want.

If you also need the residue number of the Cysteines, you can get the PDB files for all human proteins and parse them to extract that information. In case you are not familiar, here's a description of disulfide annotation in the PDB file.

You can get the list of PDB IDs for all human proteins (for example from Gencode File: gencode.v21.metadata.PDB.gz). Then get the PDB files for those IDs using FTP or web service and then parse the PDB files to extract the disulfide annotation.

[Rm]

+1 for gencode list

Answer 2

[Elisabeth Gasteiger]

You can get this data from UniProt using the following query (using the advanced search for example):

http://www.uniprot.org/uniprot/?query=annotation%3A%28type%3Adisulfid%29&sort=score

You can further filter this result, e.g. by organism or by evidence (use the advanced search again), and download the data in various formats.

[Rm]

Thanks @siva and @Elisabeth for your inputs: customisable table search in uniprot is very useful. We can add disulphide bond within PTM/processing column selection