Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry

Nucleic Acids Res. 2010 Jan;38(Database issue):D320-5. doi: 10.1093/nar/gkp1013. Epub 2009 Nov 11.

Abstract

The backbone bond lengths, bond angles, and planarity of a protein are influenced by the backbone conformation (varphi,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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Amino Acid Motifs
  • Animals
  • Catalytic Domain
  • Computational Biology / methods*
  • Computational Biology / trends
  • Databases, Genetic*
  • Databases, Nucleic Acid*
  • Databases, Protein*
  • Humans
  • Information Storage and Retrieval / methods
  • Internet
  • Peptides / chemistry
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Software

Substances

  • Peptides
  • Proteins