2008/6/14 Bour, Stephan (NIH/NHLBI) [E] <[EMAIL PROTECTED]>: > You may want to check out the DAVID set of tools from the National Institute > of Allergy and Infectious Diseases. It was originally designed to address > this kind of issue. > http://david.abcc.ncifcrf.gov/
How do you mean? > Stephan. > > > -----Original Message----- > From: Dan Bolser [mailto:[EMAIL PROTECTED] > Sent: Sat 6/14/2008 9:42 AM > To: General Forum at Bioinformatics.Org > Subject: Re: [BiO BB] how pdb ID is defined? > > On 27/05/2008, Xue Li <[EMAIL PROTECTED]> wrote: >> Dear all, >> >> Maybe this is a naive question. I just noticed that proteins 2GSA and >> 4GSA have similar name and denote almost the same protein. >> >> 4gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE >> (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE >> 2gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE >> AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM) >> >> Also, 2ae2 and 1ae1 denote similar proteins. >> 2ae2: TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE >> 1ae1: TROPINONE REDUCTASE-I COMPLEX WITH NADP >> >> >> Would someone please tell me how PDB ID is defined? Given a list of >> pdb ID, can I find biological distance merely based on their pdb IDs? > > In 'the old days' PDB ID's were chosen by the author, and 'updated' > versions of the same protein were indexed by their first digit.. i.e. > 1sod / 2sod / etc. for the SuperOxide Dismutase structures. > > These days the id is arbitrary as you discovered. > > There is a page dealing with this question on PDBWiki: > http://pdbwiki.org/index.php/PDB_code > > Which is part of the PDB FAQ that is collaboratively maintained there: > http://pdbwiki.org/index.php/PDB_FAQ > > HTH, > > Dan. > > >> >> Thanks a lot. >> >> -- >> Xue, Li >> Bioinformatics and Computational Biology program @ ISU >> Ames, IA 50010 >> 515-450-7183 >> >> _______________________________________________ >> BBB mailing list >> [email protected] >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > -- > hello > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > > -- hello _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
