title: Comparison of spatial arrangements of secondary structural elements in proteins.
abstract: We have developed a new method of protein structure comparison based on spatial arrangements of secondary structural elements (SSEs). Each SSE is represented by a single vector, and common spatial arrangements of vectors in a pair of proteins are detected. The method allows not only insertions and deletions of SSEs, but also topological permutations. It has a flexible target function that can be adjusted depending upon particular levels or definitions of structural similarity, and it is fast enough to allow structural comparisons for many pairs of proteins. The parameters for the target function are determined based on distributions of the geometrical variables for the spatial arrangements of the equivalent SSEs in well-known structural motifs. The obtained parameter set is tuned for detecting relatively strong structural similarity. We report several tests on examples including comparisons of known structural similarity and database searches for a target structure, and examine the results when this parameter set is used for the comparison of distantly related structures.
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Mizuguchi
authors.forename: N
authors.initials: N
authors.lastname: Go
mesh_terms: D000426:Alcohol Dehydrogenase / Q000737:chemistry; D000465:Algorithms; D001400:Azurin / Q000737:chemistry; D001665:Binding Sites; D005981:Glutathione Synthase / Q000737:chemistry; D007770:L-Lactate Dehydrogenase / Q000737:chemistry; D008433:Mathematics; D008958:Models, Molecular; D010970:Plastocyanin / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins; D001400:Azurin; D010970:Plastocyanin; D000426:Alcohol Dehydrogenase; D007770:L-Lactate Dehydrogenase; D005981:Glutathione Synthase