searching the pdb codes from the folded proteins

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searching the pdb codes from the folded proteins

Postby TheIan » Fri May 18, 2012 3:41 pm

hi

i have a question regarding the folded proteins. i think each protein folded must have a pdb code like projekt 101 on
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http://fah-web.stanford.edu/cgi-bin/allprojects#590
. on this side are only a few codes.
i ask bekause the side
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http://jmol.sourceforge.net/fah/
loads to every projekt the protein in jmol. what i want to do is to find further information to some projects proteins over this pdb entrys. is there any side or something where i can find the pdb codes? i am sorry for the codebox but this is my first day here and i cant post urls.

thanks for help
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Re: searching the pdb codes from the folded proteins

Postby TheIan » Wed May 23, 2012 4:06 pm

does realy nobody have an anwer to my question??
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Re: searching the pdb codes from the folded proteins

Postby smoking2000 » Wed May 23, 2012 4:35 pm

The project numbers are not PDB entries, the proteins studied by FAH are not submitted to the protein database.

Additional information about the FAH proteins is only listed on the project detail page you've already found.

If a project is not listed there, you can try the project specific page at:
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http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=<PROJECT NUMBER>
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Re: searching the pdb codes from the folded proteins

Postby Jesse_V » Wed May 23, 2012 4:43 pm

I haven't seen statement that Folding@home deposits proteins in the Protein Data Bank. If they do, I'd be interested in learning about it, and then of course they'd have the PDB code. I don't think JMol looks up the protein in the PDB but it simply has a file which represents the shape of that particular protein (the extension might be .xyz). Then it renders it for you.

What do you mean by "on this side are only a few codes"? Just out of curiosity, why would you want the PDB codes anyway?

smoking2000 wrote:Additional information about the FAH proteins is only listed on the project detail page you've already found.

When the scientist first releases the project and posts about it on the Beta Team section of this forum, sometimes they'll provide more information than what can be found on the project description page. TheIan, you can search that subforum for the protein project number (the first number) and you may find that original post.
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Re: searching the pdb codes from the folded proteins

Postby 7im » Wed May 23, 2012 7:57 pm

TheIan wrote:does realy nobody have an anwer to my question??


Yes, of course somebody has the answer. But that someone may not visit this forum every day... patience is a virtue.

PDBs were a byproduct file created by some of the older fahcores, collected by a long dead client monitoring tool (EMIII). And the current fahcores do not create PDBs.

So there are no more additional PDBs other than those listed on the JMOL page. Sorry, not the answer you were looking for, but that is the answer. :twisted:


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Re: searching the pdb codes from the folded proteins

Postby TheIan » Mon May 28, 2012 10:46 am

The project numbers are not PDB entries

i know that and i search the the entries to the projects

... patience is a virtue.

yea you are right, i thought that 5 days are enough...but thanks for the answer

And the current fahcores do not create PDBs.

i hoped that the proteins or the domains of them are listed in the database, because it would be nice to share the information about the proteins with others. i know that the cores do not create then, but maybe the f@h team have post it there...its nice to say what they did in the single project, but it will be helpfull to have the pdb entries for further information

the proteins studied by FAH are not submitted to the protein database.

to that the simplyquestion: why not?

I don't think JMol looks up the protein in the PDB but it simply has a file which represents the shape of that particular protein (the extension might be .xyz).

Jmol is able to use both, the mentioned .xyz file and the .pdb file from the database...if u know the entry you can get the .pdb file...if the jmol on the posted side uses .xyz files than the question can also be where to get this files

What do you mean by "on this side are only a few codes"? Just out of curiosity, why would you want the PDB codes anyway?

some projects there have a pdb number/code and a lot of them not...so u know the storry about the project, but if u have the interest in further information about the protein of this project you can go to the pdb entry and maybe there are pubmed id´s or other informations...
i asked about this, because i am a bioinformatic student and for my work i want to have some additional informations to the proteins and not only the short deskription from the homepage

it woud be realy disappointing if the only information published about the projects are only these short descriptions
now someone can say that they publish "some" papers, but this is not what i mean
i dont know if you know what i want, but thanks to the answers
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Re: searching the pdb codes from the folded proteins

Postby 7im » Mon May 28, 2012 1:18 pm

As I said, there isn't any more data on that jmol site. The fahcorres don't even make xyz files anymore.

Please contact Dr. Pande at Stanford with your request.
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