Using the Protein Geometry Database, you can mine protein conformational space with a user-friendly but surprisingly flexible graphical interface. You can search for structural motifs from 1-10 residues with either broad secondary-structure types (Kabsch and Sander, 1983) or fine-grained ranges of the Φ and Ψ dihedral angles. You can additionally restrict your query by amino acid and by backbone covalent geometry. Cutoff thresholds allow you to search only well-defined residues within a nonredundant set of proteins (Hobohm et al., 1992).
Your search results appear on an interactive and attractive Ramachandran plot. Any of the residues in your motif query can be plotted, and the color indicates observation density. In addition to the observations, you can plot many other properties (primarily geometric) using the color or on the X or Y axes. Additionally, you can look at statistics for each 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 database in analyzing your results.
A unique aspect of the PGD is your ability to use as much or as little of its flexibility as you need. Many flexible databases are nearly unusable, and many simplistic databases make it impossible to ask your scientific question. The PGD has the advantages of both and disadvantages of neither because of its professionally designed interface.
The protein backbone is defined primarily by three dihedral angles: Φ, Ψ, and ω. The first two are highly rotatable and the concept of protein conformation is based on them. The third, ω, defines the planarity of the peptide bond and generally stays close to 180° or 0° (for cis peptides). All three dihedrals are searchable in the PGD.
Additionally, bond angles and lengths determine the details of peptide geometry, and their averages vary in a conformation-dependent manner (Karplus, 1996). They are labeled above as a1-a7 (angles) and L1-L5 (lengths), and you can search the PGD based on these parameters in addition to or instead of conformation.