[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




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