Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates.
CONCLUSIONS
The Evolutionary Trace Annotation (ETA) Server predicts enzymatic activity. ETA starts with a structure of unknown function, such as those from structural genomics, and with no prior knowledge of its mechanism uses the phylogenetic Evolutionary Trace (ET) method to extract key functional residues and propose a function-associated 3D motif, called a 3D template. ETA then searches previously annotated structures for geometric template matches that suggest molecular and thus functional mimicry. In order to maximize the predictive value of these matches, ETA next applies distinctive specificity filters -- evolutionary similarity, function plurality and match reciprocity. In large scale controls on enzymes, prediction coverage is 43% but the positive predictive value rises to 92%, thus minimizing false annotations. Users may modify any search parameter, including the template. ETA thus expands the ET suite for protein structure annotation, and can contribute to the annotation efforts of metaservers.


BACKGROUND
The ETA Server is a web application available at (http://mammoth.bcm.tmc.edu/eta/).
Ward
R Matthew
RM
Department of Molecular and Human Genetics, Program in Structural and Computational Biology and Molecular, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Venner
Eric
E
Daines
Bryce
B
Murray
Stephen
S
Erdin
Serkan
S
Kristensen
David M
DM
Lichtarge
Olivier
O
D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry*; D019143:Evolution, Molecular; D020407:Internet; D010802:Phylogeny; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
D004798:Enzymes; D011506:Proteins