Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

Optical properties of LiNbO3 : Cr crystals co-doped with Germanium oxide

Lithium niobate (LiNbO3) crystals doped with chromium ions show a clear green colouring reflecting the absorption profile of the dominating [Cr](Li) defect centres. A significant change in its colouration takes place when it is co-doped with other valency impurities such as Mg2+, Sc3+ and W6+, above a certain threshold concentration. This concentration singularity has been attributed to the formation of [Cr](Nb) centres coexisting with the [Cr](Li) centres. In this work, we extended the investigation on the effect of co-dopant ions in Cr:LiNbO3 to tetravalent cation such as GeO2. A singularity in the relative intensity of the (4)A(2)-> T-4(1) and (4)A(2)-> T-4(2) absorption band was observed for a concentration of similar to 1.5 mol%, compared with 4.5 mol% for Mg2+. The photoluminescence emission spectra also reveal a new emission band, at a lower energy than the [Cr](Li) centre, corresponding to this threshold concentration. A charge compensation model is proposed to explain the role of cation impurities and results are compared with those of other valence impurities