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The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB. However, I do not see any method to access this particular data.

  1. A list of each of the 1400 folds (just an id number, and/or a descriptor)?

  2. For each individual fold (of the 1400), a list of PDB IDs for proteins which are known to adopt each individual fold?

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It looks like you can download the full database in SQL format or parse-able text files from here: SCOP Download - Berkeley

The link has a link to the Schema as well:

enter image description here

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  • $\begingroup$ Thanks for the answer, but it doesn't answer the question. Being able to download the database doesn't help. The schema might have been useful - except that none of the tables have around ~1400 rows, or at all mention folds/topologies in the table name or description. $\endgroup$ – Aalawlx Mar 10 '16 at 19:06
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If there is a simple way provided to do this it is very well hidden. The tedious and stupid way to do 1 (get a list of folds) would seem to involve rolling your own:

  1. Go to http://scop.berkeley.edu/ver=2.06 .

  2. Click on each of the 12 classes in turn. e.g. (a) all alpha proteins will take you to http://scop.berkeley.edu/sunid=46456 .

  3. Save the source of each page as text.

  4. Write and run your own parser to pull out the sunid (*****) from the http://scop.berkeley.edu/sunid=***** and the description line if you wish. (This assumes you program.) I think this sunid is the fold id.

If you can than find some database or table that has PDB and sunid values in it, you can write another program to find the answer to 2.

Sorry not to be more helpful.

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