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Efforts are ongoing to extend the search base of BioPhytMol as well as to include batch query options where multiple structures can be searched using the similarity search tool for their corresponding similar structures.
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The database houses information on annotation, distribution and diversity of RNRs, and links to solved RNR structures, and can be searched through a BLAST interface.
This step preprocesses the reference sequence, creating a data structure that can be searched fast and efficiently.
Since the information composing the graph is available to the page at runtime as a data-structure, it can be searched and filtered, and the graph can been zoomed and scaled to highlight particular nodes and edges that interest the user.
Molecular structures on the internet can be searched using InChI and InChIKeys [21] directly.
Her research is a concrete example of how academics are trying to build what some call the "semantic Web," a phrase that usually applies to efforts to provide a richer, more structured collection of data that can be searched and analyzed with more precision.
When a search has to be performed by a structure of compound, the database can be searched via substructure or similarity.
This database contains potential homologues for >300,000 different proteins (http://reversehhpred.cimr.cam.ac.uk), and can be searched with structures from the Protein Data Bank (PDB).
Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability.
The most accessible and transparent approaches to prediction based on chemical structure have been expert rule-based SAR models, supported by large relational databases of toxicologic information that can be searched by chemical structure and substructure to identify analogs that can be used to make inferences about the toxicity of a new chemical (Richard et al. 2006).
ChemReader is a software developer toolkit for translating digital raster images of chemical structures into standard, chemical file formats that can be searched and analyzed with other open source or commercial cheminformatic software.
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