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Protein Geometry Database Server V 1.0
http://pgd.science.oregonstate.edu/
Developed by Andy Karplus' laboratory at Oregon State University
We are pleased to announce the availability of an enhanced version
of the Protein Geometry Database (PGD) web service, originally
announced in Berkholz et al (2010) Nucleic Acids Research 38, D320-5.
This server allows you to explore the many backbone and side chain
conformations that exist in the PDB as well as the protein geometry
(lengths and angles) that occur in those conformations. This service
is ideal for finding instances of particular conformations or peculiar
bond lengths or angles. It is also quite adept at identifying sets of
fragments that can then be examined for systematic variation in
"ideal" geometry. The expanded PGD now includes all conformational and
covalent geometry information not just for the backbone but also for
the sidechains.
There are three basic operations available: selecting a set of
fragments via a delimited search, analyzing the geometry of those
fragments, and dumping the results to your computer for more
specialized analysis.
To control bias in statistical analyses due to the variable number
of entries with the same or similar sequence, the database contains
only the highest quality model in each sequence cluster as identified
by the Pisces server from Roland Dunbrack's lab. Two settings, 90%
and 25% sequence identity, are available. Currently, at the 90%
sequence identity level there are 16,000 chains and at the 25% level
this drops to about 11,000 chains.
You can filter a search based on the quality of the model as
indicated by resolution and R values. A search can also be filtered
based on DSSP secondary structure, amino acid type, the phi/psi/omega
angles and bond lengths, angles, and chi angles. For example, you can
find all cysteine residues in the center of three-residue peptide
fragments (i.e. not at a peptide terminus), in beta sheet, with both
peptide bonds trans, and CB-SG length greater than 1.85 A from models
with resolution better than 1.5 A. By the way, in the "no more than
25% sequence identity" category there are 25 of them.
Once you have a set of results, you can create 2D plots showing the
relationships of up to three features (i.e. bond lengths, bond angles,
or conformational angles). For instance, you can look at how a given
feature varies with phi and psi using a phi(i)/psi(i) plot. Or, you
can just as easily look at the variation with psi(i)/phi(i+1), or even
the relationships between any selected bond angles. As one example,
it is instructive to perform a default search and plot NCaCb vs NCaC
colored based on CbCaC. As this search is restricted to just the
highest resolution models, you can see the justification for chiral
volume restraints.
Finally, all of your results can be downloaded for your own analysis.
Development of the PGD continues. If you have worked with the site
and have any ideas and suggestions for how to improvement it, please
drop us a line.
The publication describing the PGD is:
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 with covalent geometry.
Nucleic Acids Res. 38, D320-5.
Also, some examples of published analyses enabled by earlier
versions of the PGD are listed here:.
Berkholz, D.S., Shapovalov, M.V., Dunbrack, R.L.J. & Karplus, P.A.
(2009). Conformation dependence of backbone geometry in proteins.
Structure 17, 1316-1325.
Hollingsworth, S.A., Berkholz, D.S. & Karplus, P.A. (2009). On the
occurrence of linear groups in proteins. Protein Science 18, 1321-1325
Hollingsworth, S.A. & Karplus, P. A. (2010). Review: A fresh look at
the Ramachandran plot and the occurrence of standard structures in
proteins. BioMolecular Concepts 1, 271-283.
Berkholz, D.S., Driggers, C.M., Shapovalov, M.V., Dunbrack, R.L., Jr.
& Karplus P.A. (2012) Nonplanar peptide bonds in proteins are common
and conserved but not biased toward active sites. Proc Natl Acad Sci U
S A. 109, 449-53.
Dale Tronrud & P. Andrew Karplus
Department of Biochemistry and Biophysics
Oregon State University
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