SABERTOOTH: protein structural alignment based on a vectorial structure representation

Background: The task of computing highly accurate structural alignments of proteins in very short computation time is still challenging. This is partly due to the complexity of protein structures. Therefore, instead of manipulating coordinates directly, matrices of inter-atomic distances, sets of vectors between protein backbone atoms, and other reduced representations are used. These decrease the effort of comparing large sets of coordinates, but protein structural alignment still remains computationally expensive. Results: We represent the topology of a protein structure through a structural profile that expresses the global effective connectivity of each residue. We have shown recently that this representation allows explicitly expressing the relationship between protein structure and protein sequence. Based on this very condensed vectorial representation, we develop a structural alignment framework that recognizes structural similarities with accuracy comparable to established ali...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Florian Teichert, Ugo Bastolla, Markus Porto
• Keywords: BMCBI 2007, Protein, Protein Structures, Structural