Protein Geometry Database: a Flexible Engine to Explore Backbone Conformations and Their Relationships to Covalent Geometry

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2009 Nov 13

PMID 19906726

Citations 20

Authors

Donald S Berkholz

Peter B Krenesky

John R Davidson

P Andrew Karplus

Affiliations

Soon will be listed here.

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.

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