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
