Question: How Can I Get All The Domain Structures In A Cath Superfamily?
6
gravatar for Simon Cockell
8.9 years ago by
Simon Cockell7.3k
Newcastle
Simon Cockell7.3k wrote:

I want to retrieve all of the PDB files for domains that belong to a particular superfamily in the CATH database.

I can get representative structures of families from the CATH download area, I can also get lists of domains and domain boundaries, so I can construct them myself by pulling files from the PDB and trimming programatically, but I was wondering if anyone here has come up with a more efficient method?

I'll proceed with writing the code and post it as an answer once I'm done, but maybe someone can provide me with a better solution in the meantime.

pdb database • 3.7k views
ADD COMMENTlink modified 4.6 years ago by Biostar ♦♦ 20 • written 8.9 years ago by Simon Cockell7.3k

Hi, Andy from CATH here :-)

Do you mean the original whole-protein PDBs from which the domains were extracted, or the chopped PDBs we produce that just contain individual domains?

ADD REPLYlink written 8.9 years ago by Andrew Clegg310
12
gravatar for Andrew Clegg
8.9 years ago by
Andrew Clegg310
London
Andrew Clegg310 wrote:

Sorry, ignore my (deleted) comment, I read your question again and saw the bit about trimming.

Once you have the domain list, you can hit this URL to get an individual domain:

http://www.cathdb.info/api/data/pdb/1cukA01

Where 1cukA01 is the domain in question. Or for a whole chain:

http://www.cathdb.info/api/data/pdb/1cukA

... or indeed a whole pdb the same way.

We're adding this to the docs at the moment, didn't realise it wasn't in there :-)

Also planning to add a REST service to get all the members of a superfamily via HTTP, but you can parse this out of the domain list as you spotted.

ADD COMMENTlink written 8.9 years ago by Andrew Clegg310
3

It's a couple of years since I used CATH. I'm amazed and impressed by its transformation.

ADD REPLYlink written 8.9 years ago by Neilfws48k

that's perfect! I love BioStar...

ADD REPLYlink written 8.9 years ago by Simon Cockell7.3k

Thanks Neil -- spread the love :-)

ADD REPLYlink written 8.9 years ago by Andrew Clegg310

PS... You should see the next version (end of this year)

ADD REPLYlink written 8.9 years ago by Andrew Clegg310
6
gravatar for Simon Cockell
8.9 years ago by
Simon Cockell7.3k
Newcastle
Simon Cockell7.3k wrote:

The code I used for the answer to this question is can be found here.

Much simpler code than I thought would be necessary, thanks to Andrew :)

ADD COMMENTlink modified 11 days ago by RamRS24k • written 8.9 years ago by Simon Cockell7.3k
0
gravatar for Jmdana
8.1 years ago by
Jmdana0
Jmdana0 wrote:

This answer arrives very late but it could help others.

PDBe has a service called PDBeXplore. This service cross-references data between different databases/classification systems and PDBe (one of those classification systems is CATH).

If you go to the PDBeXplore - CATH module and select a CATH class you will be able to see all the PDB entries belonging to it. You will also be able to download the whole table as a tab delimited file (right hand panel). From there, it is very easy just to parse the file and download the PDB files one by one.

Hope that helps.

ADD COMMENTlink written 8.1 years ago by Jmdana0
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