Protein Geometry Database

The PGD allows you to explore either protein conformation or protein covalent geometry or the correlations between protein conformation and bond angles and lengths.

You can search an up-to-date database of nonredundant protein chains while selecting chains based on the R value and resolution and filtering residues based on their average B factor. You can select structural motifs up to 10 residues long with either broad secondary-structure types or fine-grained ranges of the Φ and ψ dihedral angles. You can additionally restrict your query by amino acid type, by backbone covalent geometry and/or side chain conformatonal angles.

Search results appear on an interactive plot which defaults to a Ramachandran plot. Any conformational angle, bond length, or bond angle of any of the residues in the motif can be plotted. The colors can indicate the observational density or the value of any of the other stereochemical properties of any other residue.

Additionally, you can look at statistics broken down by residue type, browse individual results, or download a plain-text dump of the results. This dump allows you to pass the output of the PGD into the analysis tool of your choice, preventing you from being limited by the capabilities of our website in analyzing your results.

Plot of phi vrs psi of the average N-CA-C angle.png Example Plot

By registering at this site, your log-on will allow you to save and recall previous searches.

Citing this resource:

Berkholz, D.S., Krenesky, P.B., Davidson, J.R., Karplus, P.A. (2010) Protein geometry database: a flexible engine to explore backbone conformations and their relationships to covalent geometry. Nucleic Acids Research, 38, Database issue, D320-D325.