Predictions without templates: New folds, secondary structure, and contacts in CASP5

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Abstract
We present the assessment of CASP5 predictions in the new fold category. For coordinate predictions, we considered five targets with new folds and eight lying on the fold recognition borderline. We performed detailed visual and numerical comparisons between predicted and experimental structures to assess prediction accuracy. The two procedures largely agreed, but the visual inspection identified instances where metrics, such as GDT_TS, ranked what we considered incorrect predictions highly. We found the quality of the best predictions to be very good: for nearly every target at least one group predicted a structure close to the correct one. However, selection of the best of five models is still problematic. The group of David Baker once again proved to be best overall, with many individual highlights. However, high quality and consistency were also seen from others, suggesting that the community is moving toward general procedures to predict accurate structures for proteins showing no resemblance to anything seen before. Predictions for secondary structure showed at best limited progress since CASP4. The number of targets is probably too small to spot differences in performance between methods, suggesting that such predictions might be better evaluated with schemes involving more proteins. For contact predictions, accuracies are still low, although there were several instances of accurate and useful contacts predicted de novo, and new approaches hint at future progress. Proteins 2003;53:436–456.