Structural alphabets derived from attractors in conformational space

Background: The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as `states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis. Results: A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attrac...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Alessandro Pandini, Arianna Fornili, Jens Kleinjung
• Keywords: BMCBI 2010, Protein Structure, Proteins, Structural Alphabet