I want to list all proteins in the protein database and list them by the ratio of number of disulphide bonds per peptide bond. I am not particular about the reliability of identification of disulphide bond.

--EDIT 1 I've been doing some research on this topic, and heres what i've found.

  1. The PDB structure file lists all the Disulphide bonds in each structure.(SSBOND)

  2. The PBD structure file does not list the number of peptide bonds, however it does mention the number of amino acids. And number of peptide bonds = [no. of amino acids - 1].

  3. We can generate a list of all PDB structure IDs with atleast 1 disulphide bond, using PDB.org's advanced search feature. This gives a list of 22543 structures.

  4. Downloading all the 22543 structures and then parsing them using any programming language would be easy, except for the difficulty of downloading all the 22543 sturctures.

So the question now is: How do I parse all the 22543 structures to output only the number of disulphide bonds and the number of amino acids in each chain, without downloading the PDB structure files?


closed as off-topic by WYSIWYG, Chris, fileunderwater, AliceD, One Face Mar 3 '15 at 13:32

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  • $\begingroup$ Count the number of cysteines and divide by total number of amino acids- that would be a not so reliable method. $\endgroup$ – WYSIWYG Mar 2 '15 at 13:46
  • $\begingroup$ That is the obvious answer for a single protein. I am looking for a way to do it across all the proteins in the PDB. Essentially I want a way to query the number of Disulphide bonds from all proteins and the number of amino acids from all the proteins, and print a list. $\endgroup$ – user8338 Mar 2 '15 at 15:59
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    $\begingroup$ You can download all sequences from the PDB in one file: (gzipped fasta format) $\endgroup$ – Mad Scientist Mar 2 '15 at 16:03
  • $\begingroup$ Thanks Mad Scientist, I did not realize that it would be such a small file. I guess i'll have to do a little bit of coding to get the rest of the answer. $\endgroup$ – user8338 Mar 2 '15 at 16:11
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    $\begingroup$ I'm voting to close this question as off-topic because it is about text-parsing. $\endgroup$ – WYSIWYG Mar 3 '15 at 6:05