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

Dieterich, Guido ; Heinz, Dirk W. ; Reichelt, Joachim

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
The 3D structures of biomacromolecules stored in the Protein Data Bank were correlated with different external, biological information from public databases. We have matched the feature table of SWISS-PROT entries and a local version of InterProScan with the corresponding 3D-structures. OMIM (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 comparison of protein structures stored in DALI was condensed into in 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 readily identified upon visualization.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Dieterich, Guido ; Heinz, Dirk W. ; Reichelt, Joachim  (2004)  Matching of PDB chain sequences to information in public databases as a prerequisite for 3D functional site visualization. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 1(1), 2004

Online-Journal: http://journal.imbio.de/index.php?paper_id=7
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2007/188



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