CAFASP3 in the spotlight of EVA.

TitleCAFASP3 in the spotlight of EVA.
Publication TypeJournal Article
Year of Publication2003
AuthorsEyrich, VA, Przybylski, D, Y Y Koh, I, Graña, O, Pazos, F, Valencia, A, Rost, B
Volume53 Suppl 6
Date Published2003
KeywordsAlgorithms, Computational Biology, Protein Folding, Protein Structure, Secondary, Proteins, Sensitivity and Specificity

We have analysed fold recognition, secondary structure and contact prediction servers from CAFASP3. This assessment was carried out in the framework of the fully automated, web-based evaluation server EVA. Detailed results are available at We observed that the sequence-unique targets from CAFASP3/CASP5 were not fully representative for evaluating performance. For all three categories, we showed how careless ranking might be misleading. We compared methods from all categories to experts in secondary structure and contact prediction and homology modellers to fold recognisers. While the secondary structure experts clearly outperformed all others, the contact experts appeared to outperform only novel fold methods. Automatic evaluation servers are good at getting statistics right and at using these to discard misleading ranking schemes. We challenge that to let machines rule where they are best might be the best way for the community to enjoy the tremendous benefit of CASP as a unique opportunity for brainstorming.

Alternate JournalProteins
PubMed ID14579345
Grant List5-P20-LM7276 / LM / NLM NIH HHS / United States
R01-GM63029-01 / GM / NIGMS NIH HHS / United States