Abstract:
BACKGROUND:The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity. RESULTS:Here we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0), for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes. CONCLUSION:We suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file. AVAILABILITY:http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
von Grotthuss M,Plewczynski D,Ginalski K,Rychlewski L,Shakhnovich EIdoi
10.1186/1471-2105-7-53keywords:
subject
Has Abstractpub_date
2006-02-06 00:00:00pages
53issn
1471-2105pii
1471-2105-7-53journal_volume
7pub_type
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