Structure similarity searching

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The distribution of Tanimoto indices for randomly selected (or all) pairs of structures characterizes the diversity of a chemical structure database (Demuth et al. 2004 Scsibrany et al. 2003). For structure similarity searches, a number of other similarity measures have been suggested (Gasteiger and Engel 2003 Willett 1987). 

Karakoc, E., Cherkasov, A., and Sahinalp, S.C. (2006) Distance based algorithms for small biomolecule classification and structural similarity search. Bioinformatics 15,243-251. 

The prediction of the secondary structures can be made by the structure similarity search of PDB collection at the site. Several servers provide such prediction method. The Jpred, which aligns the query sequence against PDB library, can be accessed at http //jura.ebi.ac.uk 8888/index.html. To predict the secondary structures, however, check Bypass the current Brookhaven Protein Database box and then click Run Secondary Structure Prediction on the home page of Jped to open the query page (Figure 12.10). Upload the sequence file via browser or paste the query sequence into the sequence box. Enter your e-mail address (optional) and click the Run Secondary Structure Prediction button. The results with the consensus structures are returned either online (linked file) or via e-mail (if e-mail address is entered). 

Conduct the structural similarity search for a protein with the following sequence ... 

PubChem is organized as three linked databases within the NC8I s Entrez information retrieval system. These are PubChem Substance. PubChem Compound, and PubChem BioAssay. Pubchem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links above. 

The structure of a TRAF-C domain was first revealed from the crystal structure of the TRAP domain of human TRAF2 (Fig. 2A, E), alone and in complex with a receptor peptide from TNF-R2 (Park et al, 1999). The main structural architecture of the TRAF-G domain comprises an eight-stranded anti-parallel /3-sandwich, with strands j3, f38, (35, and (36 in one sheet and (32, (3S, (34, and (31 in the other. Visual inspection of the SCOP structure database (Murzin et al, 1995) and an automatic structural similarity search with the Dali program (Holm and Sander, 1995) showed that the TRAF-G domain represent a novel fold for an eight-stranded anti-parallel /3-sandwich. However, the topology observed... 

The ease of use of structure similarity search means that chromatographers can mine these tools for organizational and/or published knowledge in this area in a few seconds. 

Superstructure Search. Modification of substructure search in which the substructure query becomes the target structure, and the target structure in the database becomes the substructure search query. The search finds structures in the database that are substructures of the query. A similar extension to structure similarity searching yields superstructure similarity searching. 

Judson, P.N. (1992b). Structural Similarity Searching Using Descriptors Developed for Structure-Activity Relationship Studies. J.Chem.Inf.Comput.ScL,32,657-663. 

Judson, P.N. (1992b) Structural similarity searching using descriptors developed for structure-activity relationship studies. I. Chem. Inf. Comput. Sci., 32, 657-663. 

Key words Structural similarity search, Target prediction, Functional analysis, Pathway analysis,... 

An expansion of structural similarity searching to allow search by chemical substructures in also available as a feature of the Search Compound By Structure function (Advanced Search) of... 

If QSAR predictions and similarity searching are to be applied to the predicted metabolites of the query compound, select these options under Advanced options. By default the structural similarity search returns only compounds with one or more associated protein targets. There is also an option here to return similar molecules that do not have any associated targets. 

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