A new version of the Protein Geometry Database (PGD) has just been released.
This version includes
- The ability to compose queries and analyze the behavior of side chain
chi angles.
- Structures released in the wwPDB up to April 8, 2010 consisting of
roughly 18,000 nonredundant protein chains from crystal structures.
That's over 1.8 million residues!
The PGD enables users to easily and flexibly query information about the
conformation alone, the backbone geometry alone, and the relationships
between them. The capabilities the PGD provides are valuable for assessing
the uniqueness of observed conformational or geometric features in protein
structure as well as discovering novel features and principles of protein
structure. So if you observe a certain conformation or geometric feature
and wonder how unusual it is, the PGD may be able to provide the answer.
Queries can be based on amino acid type, secondary structure,
phi/psi/omega/chi angles, B factors and main chain bond lengths and
angles. Queries for motifs of up to 10 residues in length can be made.
Once a query has been made, plots can be drawn to show the relationship
between any pair of conformational angles and/or main chain bond lengths
or angles. In addition, the results of the query can be downloaded for
local analysis.
The PGD server is available at http://pgd.science.oregonstate.edu/
For more information please read
http://pgd.science.oregonstate.edu/static/pdf/Berkholz-PGD-2010.pdf
Happy hunting
|