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Matching of PDB chain sequences to information in public databases as a prerequisite for 3D functional site visualization

Guido Dieterich, Dirk W. Heinz, Joachim Reichelt, Bielefeld University, Bioinformatics, Medical Informatics Department, Bielefeld University Library, Publikationsdienste.Ub@Uni-Bielefeld.De, BieColl
2007 Journal of Integrative Bioinformatics  

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The 3D structures of biomacromolecules stored in the Protein Data Bank [1] were correlated with different external, biological information from public databases. We have matched the feature table of SWISS-PROT [2] entries as well InterPro [3] domains and function sites with the corresponding 3D-structures. OMIM [4] (Online Mendelian Inheritance in Man) records, containing information of genetic disorders, were extracted and linked to the structures. The exhaustive all-against-all 3D structure
more » ... mparison of protein structures stored in DALI [5] was condensed into single files for each PDB entry. Results are stored in XML format facilitating its incorporation into related software. The resulting annotation of the protein structures allows functional sites to be identified upon visualization.
doi:10.2390/biecoll-jib-2004-7 dblp:journals/jib/DieterichHR04 fatcat:py7musmjsrh7vp2c2ibb65wrfa
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Guido Dieterich, Dirk W. Heinz, Joachim Reichelt, Bielefeld University, Bioinformatics, Medical Informatics Department, Bielefeld University Library, Publikationsdienste.Ub@Uni-Bielefeld.De, BieColl. "Matching of PDB chain sequences to information in public databases as a prerequisite for 3D functional site visualization." Journal of Integrative Bioinformatics (2007)