A measure of success in fold recognition

Prediction of protein structure by fold recognition, or threading, was recently put to the test in a 'blind' structure prediction experiment, CASP2. Thirty-two teams from around the world participated, preparing predictions for 22 different 'target' proteins whose structures were soon to be determined. As experimental structures became available, we, as organizers of the threading competition, computed objective measures of fold-recognition specificity and model accuracy, to identify and characterize successful predictions. Here, we present a brief summary of these prediction evaluations, a tally of 'correct' predictions and a discussion of factors associated with correct predictions. We find that threading produced specific recognition and accurate models whenever the structural database contained a template spanning a large fraction of target sequence. Presence of conserved sequence motifs was helpful, but not required, and it would appear that threading can succeed whenever similarity to a known structure is sufficiently extensive.