The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation

Table 5 Predicted function for three structures from TargetDB

PDB ID	SeqFEATURE model	AUC	Site	Z-score	Cutoff	Other predictions
2EJQ	ZINC_PROTEASE.4.GLU.OE1	0.892	GLU96:A	4.574	-0.074	3D templates: probable anthrax toxin lethal factor
2OGF	EF_HAND.9.THR.OG1	0.920	THR17:D	4.675	3.370	SSM: aminopeptidase (Z-score = 2.7)
2OX6	EF_HAND.9.ASN.OD1	0.863	ASN8:B	4.102	2.498	3D templates: probable Zn enzyme

For each target, we provide the PDB identifier, the SeqFEATURE models that best hit the target, the locations hit by those models, the Z-scores, the corresponding 100% specificity Z-score cutoff for the model, and the predictions made by PROSITE, Pfram, 3D templates, and SSM. TargetDB structure 2EJQ has a high scoring zinc protease site. 2OGF and 2OX6 both had high scoring hits for calcium binding. Out of the other function prediction methods, only 3D templates and SSM had any predictions; these, however, were lower confidence.

ISSN: 1474-760X