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BP: Fachverband Biologische Physik

BP 26: Posters II

BP 26.4: Poster

Thursday, February 28, 2008, 17:00–19:30, Poster A

SABERTOOTH: Protein Structural Alignment Based on a Vectorial Structure Representation — •Florian Teichert¹, Ugo Bastolla², and Markus Porto¹ — ¹Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6-8, 64289 Darmstadt, Germany — ²Centro de Biología Molecular “Severo Ochoa”, (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain

The task of computing highly accurate structural alignments of proteins in very short computation time is still challenging. We tackle this issue that arises mostly from the complexity of protein structures by representing a protein fold’s topology in the form of a vectorial profile [1,2], consisting of only one real number per amino acid. Doing so, the alignment of spatial structures is carried out by maximizing the overlap of profile vectors. This simplification results in favourable scaling of computation time with chain length in comparison with other algorithms while we achieve an accuracy that is comparable to established alignment tools, like Dali, as we have shown [3]. The algorithm discussed is implemented in the ‘SABERTOOTH’ alignment server, freely accessible at http://www.fkp.tu-darmstadt.de/sabertooth/.

[1] F. Teichert and M. Porto, Eur. Phys. J. B 54, 131-136 (2006).

[2] U. Bastolla, A.R. Ortíz, M. Porto, and F. Teichert, (submitted).

[3] F. Teichert, U. Bastolla, and M. Porto, BMC Bioinformatics 8, 425 (2007).