polygon and membrane proteins
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 [email protected]
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 [email protected] mailto:[email protected]
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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. Pat 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 [email protected]
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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 [email protected]
Hi Pat, thanks! The PDB codes seem to be there as well (at least it seems to be the case from a quick look). Pavel. On 4/6/10 2:20 PM, Patrick Loll wrote:
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.
Pat
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 [email protected] mailto:[email protected]
------------------------------------------------------------------------
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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
[email protected] mailto:[email protected]
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On Tue, Apr 6, 2010 at 1:30 PM, Pascal Egea
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?
I think it is going to be limited by the relatively small sample size. Membrane proteins are only about 1% of the PDB, and the comparison of statistics in Polygon really needs to be filtered by resolution - which isn't going to leave many structures to compare with, especially at high resolution. -Nat
participants (4)
-
Nathaniel Echols -
Pascal Egea -
Patrick Loll -
Pavel Afonine