Question: Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
0
gravatar for Christian
4 weeks ago by
Christian0
bangalore
Christian0 wrote:

I want to Download all the HeteroComplex protein PDB IDs, which are in the Protein Data Bank. Does anybody know a python programme to do this? I mean does anybody know a programme to get all the heterocomppex PDB IDs in the protein data bank? Thanks in advance.

ADD COMMENTlink written 4 weeks ago by Christian0
1

Not directly answering your question, but maybe this will still help you. For these kinds of things I use advanced search:

http://www.rcsb.org/pdb/search/advSearch.do?search=new

You can search by multitude of criteria, individually or in combination. For example, one can select "Text Search" as a query type and enter "heterocomplex" or anything else. Additional criteria can be added to narrow down the search. When the search results are displayed, one can select a report type such as "List selected PDB IDs" which is presumably what you want. It gives 17 IDs that have "heterocomplex" somewhere in text.

ADD REPLYlink written 4 weeks ago by Mensur Dlakic2.2k

@Mensur Dlakic Thank you very much for your answer. But I want to find all the HeteroComplexes in the Protein Data Bank (all the PDB IDs which composed of two or more different types of chain. For example PDB ID XXXX which will be made up of chain A and Chain B. Not with two chain 'A's.) So there will be thousands of PDB IDs. I think this can be only done using a Python programme. Sorry my question was not clear. Thank you.

ADD REPLYlink written 4 weeks ago by Christian0
1

I have done searches that have resulted in tens of thousands of IDs, so that's not a limit on the strategy I proposed. It is only a matter of formulating the search terms properly. For example, there is a search field "Number of chains" that may do what you want in combination with other parameters.

ADD REPLYlink written 4 weeks ago by Mensur Dlakic2.2k

You are absolutely correct. I didn't realize there are these many varieties of search options in Advanced search. Thank you very much for your help.

ADD REPLYlink written 29 days ago by Christian0
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