Regensburg 2007 – scientific programme

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BP: Fachverband Biologische Physik

BP 4: Protein Structure and Folding

BP 4.7: Talk

Monday, March 26, 2007, 19:00–19:15, H43

A generalized vectorial protein structure representation and its application in structure comparison — •Florian Teichert¹, Ugo Bastolla², and Markus Porto¹ — ¹Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 8, 64289 Darmstadt, Germany — ²Centro de Biología Molecular "Severo Ochoa", (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain

A structural profile was recently proposed for single-domain protein structures [1]. We have extended this representation to include a consistent description of both single- and multi-domain folds [2], thus considerably broadening its applicability in bioinformatics. For one possible application, a so-called structure alignment scheme, we use this extended structural profile to compare three-dimensional protein folds and locate segments where similarities or differences exist. The benefit of our alignment scheme is that it is more general than existing algorithms. A first assessment shows that its performance is comparable with existing techniques. Yet, even more important, it constitutes a promising starting point for the analysis of structure/structure, sequence/structure, and sequence/sequence alignments within the same scheme.

[1] M. Porto, U. Bastolla, H.E. Roman, and M. Vendruscolo, Phys. Rev. Lett. 92, 218101 (2004) (4 pages).

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