engleski

Database of pore domain models from cationic channels

In the post-genomic proteome era, biologists often need to construct their own problem-specific databases in order to support the analysis and knowledge discovery. In this context, the database of channel proteins, with accurate structure and functional annotations, is of special interest in neuroscience, highly dynamic and overwhelming research area. Here we report a customized database of pore-forming domains from cationic channels (the P-region domains) that was created by using semi-automated collection and management as well as high accuracy modeling procedure. Literature and data mining problems are exposed in connection with collecting the unique set of functional channel protein families. After clarifying these problems, the family-specific potentials for identification of new members are identified from database’ s current state of channel-protein knowledge. In the absence of more than handful of high resolution 3D structures, sequence analysis techniques are the sole solution for pore domain definition. Therefore, we built pore domain models, with modeling procedure that was based on use of several bioinformatics tools, developed with primary sequence input, and evaluated with appropriate statistical techniques. Modeled data are stored in a MySQL database which can be interactively queried over the web at URL: http://split.pmfst.hr/PPore/index.html

pore domain; cationic channel; annotation; database

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