Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry -- Berkholz et al., 10.1093/nar/gkp1013 -- Nucleic Acids Research - http://nar.oxfordjournals.org/cgi...
"The backbone bond lengths, bond angles, and planarity of a protein are influenced by the backbone conformation (phi, psi), but no tool exists to explore these relationships, leaving this area as a reservoir of untapped information about protein structure and function. The Protein Geometry Database (PGD) enables biologists to easily and flexibly query information about the conformation alone, the backbone geometry alone, and the relationships between them. The capabilities the PGD provides are valuable for assessing the uniqueness of observed conformational or geometric features in protein structure as well as discovering novel features and principles of protein structure. The PGD server is available at http://pgd.science.oregonstate.edu/ and the data and code underlying it are freely available to use and extend."
- Donnie Berkholz
from Bookmarklet
My paper just came out as advance access for the Database Issue of Nucleic Acids Research! Let me know if you're interested / have any questions.
- Donnie Berkholz
Another paper of mine was published today! That marks the 2nd in a month. It's about the Protein Geometry Database. http://nar.oxfordjournals.org/cgi...
"The Hype Cycle describes the way that new technologies and projects are perceived over time, if they do a good job of handling themselves, going from a technology trigger, inflated expectations, disillusionment, enlightenment, before arriving at “the plateau of productivity” – a state where there is no more hype and the new technology is simply a normal part of our lives." The perception over the past few years that Gentoo is dying is in reality Gentoo's arrival at the plateau of productivity. Hype has gone away and remaining is a distribution with a true niche that fits into the broader Linux ecosystem.
- Donnie Berkholz