PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
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.


CONCLUSIONS
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.


BACKGROUND
http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF.
von Grotthuss
Marcin
M
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA. mvg@paradox.harvard.edu
Plewczynski
Dariusz
D
Ginalski
Krzysztof
K
Rychlewski
Leszek
L
Shakhnovich
Eugene I
EI
D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D003628:Database Management Systems; D030562:Databases, Protein; D004789:Enzyme Activation; D004798:Enzymes / Q000032:analysis / Q000737:chemistry* / Q000145:classification / Q000378:metabolism* / Q000648:ultrastructure; D016247:Information Storage and Retrieval / Q000379:methods; D008956:Models, Chemical; D008958:Models, Molecular; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013329:Structure-Activity Relationship; D014584:User-Computer Interface
D004798:Enzymes