[BiO BB] Getting PDB id from Swissprot entry
Sourangshu Bhattacharya
sourangshu at csa.iisc.ernet.in
Fri Jul 2 14:29:17 EDT 2004
Madam,
Thank you very much for the advice.
I also found some more PDB files which are supposed to have
permutations. I am going through them. In many cases, I find there is a
repeat of domains.
Regards,
Sourangshu.
Dr.Nagasuma Chandra wrote:
>I agree too and would ask the same question that Dan asked, but dont see
>the relevance of this thread to the specific question Sourangshu asked.
>
>Sourangshu, if you are looking for the exact match, then fetching the DR
>lines is the simplest, but what Iddo said still holds good (of many-many
>matches in some cases, part domain/missing loops in some cases)- all
>depends on what you are looking for.
>
>Nagasuma Chandra
>
>***********************************************
> Dr. Nagasuma Chandra
> Bioinformatics centre
> Indian Institute of Science
> Bangalore 560 012
> Tel: +91-80-22932469 or 23601409
> Fax: +91-80-23600551
> e-mail: nchandra at physics.iisc.ernet.in
>***********************************************
>
>
>On Fri, 2 Jul
>2004, Dan Bolser wrote:
>
>
>
>>On Thu, 1 Jul 2004, D. Norris wrote:
>>
>>
>>
>>>Hi:
>>>
>>>Meaningful bioinformatics must work in the whole cell, and whole
>>>multicellular organism. Genomics and proteomics alone are just lists of
>>>parts--no more, no less !!!
>>>
>>>
>>I agree, but can you suggest a 'whole cell' or 'organism' framework that I
>>can use?
>>
>>dan
>>
>>
>>
>>>dmn
>>>----- Original Message -----
>>>From: "Dan Bolser" <dmb at mrc-dunn.cam.ac.uk>
>>>To: <bio_bulletin_board at bioinformatics.org>
>>>Cc: <ssml at bioinformatics.org>
>>>Sent: Wednesday, June 30, 2004 8:32 AM
>>>Subject: Re: [BiO BB] Getting PDB id from Swissprot entry
>>>
>>>
>>>
>>>
>>>>On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote:
>>>>
>>>>
>>>>
>>>>>Hi,
>>>>>
>>>>>Is there a direct way (without reading the protein name from swissprot
>>>>>and searching in PDB) of getting the PDB id of the protein corresponding
>>>>>to a particular Swissprot id ?
>>>>>
>>>>>
>>>>I would use the MSD database, which maintains a manually curated version
>>>>of the SwissProt to PDB mapping.
>>>>
>>>>
>>>>
>>>>>Also, how do I know whether structure for a particular protein
>>>>>corresponding to a swissprot id has been determined or not ?
>>>>>
>>>>>
>>>>Strictly speeking, the above mapping gives you this. More realistically,
>>>>however, you can consider very close homologues to the above set as also
>>>>'solved'. Where you draw the line is a matter of requirement, but you can
>>>>get reasonable models (allegedly) at > 40% sequence identity, or
>>>>reasonable 'fold prediction' at much larger distances (see SUPERFAMILY for
>>>>example).
>>>>
>>>>It all depends on what you want to do.
>>>>
>>>>
>>>>
>>>>>Thank you very much..
>>>>>
>>>>>Regards,
>>>>>Sourangshu.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>_______________________________________________
>>>>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
>>>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>>>
>>>>
>>>_______________________________________________
>>>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
>>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>>
>>>
>>>
>>_______________________________________________
>>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>>
>>
>
>
>_______________________________________________
>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
--
Sourangshu Bhattacharya
PhD Student,
Dept. of Computer Science & Automation,
Indian Institute of Science,
Bangalore - 560012, India.
Website: http://people.csa.iisc.ernet.in/sourangshu
Cell Phone : 91-98457 97492
More information about the BBB
mailing list