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1 Stockholm Bioinformatics Center, Stockholm University, SE 10691 Stockholm, Sweden
2 International Institute of Molecular and Cellular Biology, 02-109 Warsaw, Poland
Reprint requests to: Dr. Arne Elofsson, Stockholm Bioinformatics Center, Stockholm University, SE 10691 Stockholm, Sweden; e-mail: arne{at}sbc.su.se; fax: 46-8-15-8057.
During recent years many protein fold recognition methods have been developed, based on different algorithms and using various kinds of information. To examine the performance of these methods several evaluation experiments have been conducted. These include blind tests in CASP/CAFASP, large scale benchmarks, and long-term, continuous assessment with newly solved protein structures. These studies confirm the expectation that for different targets different methods produce the best predictions, and the final prediction accuracy could be improved if the available methods were combined in a perfect manner. In this article a neural-network-based consensus predictor, Pcons, is presented that attempts this task. Pcons attempts to select the best model out of those produced by six prediction servers, each using different methods. Pcons translates the confidence scores reported by each server into uniformly scaled values corresponding to the expected accuracy of each model. The translated scores as well as the similarity between models produced by different servers is used in the final selection. According to the analysis based on two unrelated sets of newly solved proteins, Pcons outperforms any single server by generating 
8%–10% more correct predictions. Furthermore, the specificity of Pcons is significantly higher than for any individual server. From analyzing different input data to Pcons it can be shown that the improvement is mainly attributable to measurement of the similarity between the different models. Pcons is freely accessible for the academic community through the protein structure-prediction metaserver at http://bioinfo.pl/meta/.
Keywords: Fold recognition; threading; benchmark; web servers; LiveBench; CASP; CAFASP
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