[phenixbb] polygon and membrane proteins

Patrick Loll pat.loll at drexel.edu
Tue Apr 6 14:20:29 PDT 2010

I don't know how easy this would be to do, but...

Steve White maintains a nice up-to-date database of membrane proteins  
of known structure (http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html 
). Since he has tabulated all of the PDB IDs, it should be trivial for  
him to supply just a list of the four-letter codes, which could be  
used as a filter.


On 6 Apr 2010, at 5:08 PM, Pavel Afonine wrote:

> Hi Pascal,
> what are the selection criteria that can be used to identify those  
> structures in PDB? Any specif keywords in PDB file header? Can it be  
> done (such a selection) in a robust way (with minimum guesses and  
> resulting errors)?
> If you can formulate these selection criteria, then I will be able  
> to add it to a future version.
> Pavel.
> On 4/6/10 1:30 PM, Pascal Egea wrote:
>> Dear Developers,
>> I wonder if there would be a simple way to get the Polygon program  
>> implemented in Phenix to use only membrane protein deposited  
>> structures as the reference data set. I understand that the  
>> reference set is much smaller than the whole menagerie of available  
>> structures but it represents an homogenous class of protein  
>> (crystallized in detergent).
>> Do you think that this would be meaningful and useful?
>> Thanks in advance,
>> -- 
>> Pascal F. Egea, PhD
>> Assistant Professor
>> UCLA, David Geffen School of Medicine
>> Department of Biological Chemistry
>> 314 Biomedical Sciences Research Building
>> office (310)-983-3515
>> lab (310)-983-3516
>> email pegea at mednet.ucla.edu
>> _______________________________________________
>> phenixbb mailing list
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Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pat.loll at drexelmed.edu

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