Re: [ccp4bb] pdb-l: Sequence Location in Protein Tertiary Structure

Protein crystallography Programs for crystallography X-ray detectors
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CCP4bb <-- 2007 <-- April 2007 <-- 03 April 2007

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Subject: Postdoctoral position, Division of Structural Biology, Oxford
From: Robert Gilbert gilbert {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-04-03

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From: Joerg Kallen joerg {- dot -} kallen {- at -} NOVARTIS {- dot -} COM
Date: 2007-04-04

Subject: Re: pdb-l: Sequence Location in Protein Tertiary Structure
From: Lucas Bleicher lbleicher {- at -} YAHOO {- dot -} COM
Date: 2007-04-03

By the way, I'll extend that question: the validation
software Verify3D assigns not only buried state but
also polar fraction and secondary structure, using the
probability of finding given residues in the different
"environment" defined when combining all this
information to calculate a "score" of protein regions,
which could identify, for example, sequence
misthreading. The program is rather old (1991) and,
aside from the automated validation site at UCLA
(which just let you upload a PDB and get the scores),
I haven't found a web page for it. Is there available
code to assign residues to one of those "environments"
and updated probabilities of finding amino acids in
each one?

Lucas

Wei Huang wrote:
> Hi all,
>
> Do someone know a tool which could identify the
> location of the sequence in
> tertiary structure known protein, that is the
> sequence is on the surface or
> in the
> core? Usually we use visualization tools, such as
> RasMol, VMD, to identify this
> by our eyes. But I don't know whether there are
> tools that we could input PDB
> file and the sequence only, then the computer
> tells us the sequence is on the
> surface or in the core.

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CCP4bb <-- 2007 <-- April 2007 <-- 03 April 2007

Previous message:
Subject: Postdoctoral position, Division of Structural Biology, Oxford
From: Robert Gilbert gilbert {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-04-03

Next message:
Subject: Crystallization position, 25793BR, Novartis Pharma, Basel (Switzerland)
From: Joerg Kallen joerg {- dot -} kallen {- at -} NOVARTIS {- dot -} COM
Date: 2007-04-04