Use of a structural alphabet for analysis of short loops connecting repetitive structures

Background: Because loops connect regular secondary structures, analysis of the former depends directly on the definition of the latter. The numerous assignment methods, however, can offer different definitions. In a previous study, we defined a structural alphabet composed of 16 average protein fragments, which we called Protein Blocks (PBs). They allow an accurate description of every region of 3D protein backbones and have been used in local structure prediction. In the present study, we use this structural alphabet to analyze and predict the loops connecting two repetitive structures. Results: We first analyzed the secondary structure assignments. Use of five different assignment methods (DSSP, DEFINE, PCURVE, STRIDE and PSEA) showed the absence of consensus: 20% of the residues were assigned to different states. The discrepancies were particularly important at the extremities of the repetitive structures. We used PBs to describe and predict the short loops because they can help a...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Laurent Fourrier, Cristina Benros, Alexandre G. de Brevern
• Keywords: Assignment Methods, BMCBI 2004, Secondary Structure, Structural Alphabet