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 structures of all but three of these 23 targets revealed substantial similarities to known structures, with at least eleven of the target structures likely being distantly homologous to known structures. Nineteen of the 23 target structures 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 remaining four targets were obtained afterwards. The predicted three‐dimensional structures for each of the 23 targets were analyzed to select those predictions sharing with the experimental structures a similar overall fold and/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 classified 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 target. 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 different prediction methods in the fold prediction/recognition category. Proteins Suppl 1999;3:88–103. © 1999 Wiley‐Liss, Inc.