Structure classification-based assessment of CASP3 predictions for the fold recognition targets

The sequences of at least 23 of the 43 CASP3 targets showed no significant similarity to the sequences of known structures. The experimental structure s of all but three of these 23 targets revealed substantial similarities to known structures, with at least eleven of the target structures likely bei ng distantly homologous to known structures. Nineteen of the 23 target stru ctures were available at the time of the final CASP3 meeting in Asilomar in December 1998, whereas the experimental data on the protein folds of the r emaining four targets were obtained afterwards. The predicted three-dimensi onal structures for each of the 23 targets were analyzed to select those pr edictions sharing with the experimental structures a similar overall fold a nd/or having correctly folded a substantial fraction of the target sequence . Initially predicted models were numerically evaluated and the evaluation results aided the selection process. Each target structure was then classif ied to identify a minimal set of structural features characteristic to its protein fold and evolutionary superfamily. The predictions containing this set were assessed comparatively to find the best predictions for each targe t. The predictions of new folds were assessed separately. The total number of the selected 'correct' predictions and the quality of these predictions were used to compare the performance of different predictor teams and diffe rent prediction methods in the fold prediction/recognition category, (C) 19 99 Wiley-Liss, Inc.