I have wanted for some time to search for catalytic-triad-like configurations by defining three Ca-Cb bonds from known catalytic triads, then searching the pdb for matches, but have not thought of a quick and/or easy way to do this--can your software do this sort of thing, or is there some other software which could be used for this?
JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Friday, June 27, 2014 4:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] New Version of the Protein Geometry Database Now Available -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlOt044ACgkQU5C0gGfAG12aZACdG68Vyjw7JJimw0ofMZrJQLu8 B1IAn0Q5xx8ptRosgMXswdYmdjNKyFkA =D63d -----END PGP SIGNATURE-----
