Loops at the Protein Geometry Database
Modeling loops in a protein structure can be quite difficult due to their mobility. A number of questions can arise when building a loop such as if it is known, common or unique? Also how can one search for similar loops from existing structures?
The Protein Geometry Database (PGD) can be helpful in answering these questions (ref). The PGD allows users to search for chains up to 10 residues in length and be refined by composition, conformation (alpha helix, 3-10 helix, etc), mobility (using B factors), bond angles and lengths.
The search thresholds can be adjusted to allow for a lot of flexibility. The database contains structures that are 3 angstroms or better and currently contains about 16,000 protein chains. Finally, if you register for the site your searches can be saved for later viewing.
Donnie Berkholz
July 5th, 2010 at 7:58 PM #
Glad to hear you came across our work!
If anyone has questions or suggestions regarding the PGD, please let me know and I’ll ensure that they are addressed.
It’s also worth noting that this work was instrumental in our development of improved crystallographic refinement techniques that account for changes in backbone geometry as a function of the phi and psi torsion angles. See Tronrud, Berkholz and Karplus, Acta Cryst D66: 834-842. (2010).
Artem
July 7th, 2010 at 5:05 PM #
need direct plugin into Coot