title: SEGA: semiglobal graph alignment for structure-based protein comparison.
abstract: Comparative analysis is a topic of utmost importance in structural bioinformatics. Recently, a structural counterpart to sequence alignment, called multiple graph alignment, was introduced as a tool for the comparison of protein structures in general and protein binding sites in particular. Using approximate graph matching techniques, this method enables the identification of approximately conserved patterns in functionally related structures. In this paper, we introduce a new method for computing graph alignments motivated by two problems of the original approach, a conceptual and a computational one. First, the existing approach is of limited usefulness for structures that only share common substructures. Second, the goal to find a globally optimal alignment leads to an optimization problem that is computationally intractable. To overcome these disadvantages, we propose a semiglobal approach to graph alignment in analogy to semiglobal sequence alignment that combines the advantages of local and global graph matching.
authors.affiliation: Department of Mathematics and Computer Science, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, Marburg D-35032, Germany. mernberger@mathematik.uni-marburg.de
authors.forename: Marco
authors.initials: M
authors.lastname: Mernberger
authors.forename: Gerhard
authors.initials: G
authors.lastname: Klebe
authors.forename: Eyke
authors.initials: E
authors.lastname: Hüllermeier
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D051379:Mice; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein
chemical_list: D001426:Bacterial Proteins; D011506:Proteins