Looking for proteins with long range disulfide bonds in yeast. I reckon a database would be a good place to start, however, any publications that deal with the same may be useful as well.
You can use the reference proteome database from uniprot:
http://www.uniprot.org/uniprot/?query=taxonomy%3a559292&offset=500
In order to see proteins with annotated disulfide bonds one has to customize the results view: sequence annotation -> show -> tick Disulfide bond -> save. I saw a few proteins that have annotated disulfide bonds. If you click on the aa positions in the "Sequence annotation (DISULFIDE_BOND) " column the protein sequence would appear and the corresponding cysteines would be in yellow. Hope this helps.
You can use the reference proteome database from uniprot:
http://www.uniprot.org/uniprot/?query=taxonomy%3a559292&offset=500
In order to see proteins with annotated disulfide bonds one has to customize the results view: sequence annotation -> show -> tick Disulfide bond -> save. I saw a few proteins that have annotated disulfide bonds. If you click on the aa positions in the "Sequence annotation (DISULFIDE_BOND) " column the protein sequence would appear and the corresponding cysteines would be in yellow. Hope this helps.
sweet....still a lot of data but the filters really make a dent...Thanks again!!
if you search properly you will get some information you need: See here: http://yeastmine.yeastgenome.org/yeastmine/keywordSearchResults.do?searchTerm=%22disulfide+bond%22&searchSubmit=Search
yeah but it's just a list of publications, primarily related to oxidative folding in yeast :/ ....I was actually thinking more along the lines of a list of proteins actually containing long range disulfides, while I'm not sure that there's an automated method for identifying long range disulfides, it should be fairly simple to either manually go through all the results(assuming there aren't too many, 'many' being fairly abiguous) or to goad a Comp Sci. grad into writing a clever bit of code :D
No DB will give you the specific information you are looking for. You need to manually mine the data and extract information. an strong NLP may work!
wouldn't really need to go as far as NLP, if you mean what I think you mean...a simple spider/crawler would work fine...
Akash, you could also use Pfam. For example:
http://pfam.janelia.org/search/keyword?query=disulfide+yeast
Pfam is pretty neat!, thanks, I'd probably end up using it for more stuff as well :o so thanks a lot!!
If you are looking for long range disulfide bonds, I think the best place to find them is in the protein data bank with a filter on yeast. Point your browser to http://www.rcsb.org/pdb/home/home.do , search for "yeast", and you will find 3840 structures. Only half of these are Sacch. c. You can select these, and download the structure files as follows: Look for the blue bar with the following buttons, one page down: Filter, View, Reports, Sort. Click on the "Reports" button, and select "List selected Ids". This will return a list of the pdb ids you want to download. Save this list to a file. Run the following Perl one liner on that file: perl -pe 's/^(\S{4})\n/$1,/' yourfilename and save the results in another file. Copy and past this list into the box at http://www.rcsb.org/pdb/download/download.do , select the format you prefer, and click next. When you have all of the structure files, you can search them for disulfide information by grepping for "SSBOND" in all of the files: grep -H SSBOND *.pdb > mysslist.txt There are other ways to do this, but this should get you started.
Thank you Dr. Williams, I appreciate that you took the time to help me with my little problem, I'll try it now :),
If you are a programmer, all of this can be automated by using the pdb RESTfull Web Services at:
http://www.rcsb.org/pdb/software/rest.do
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