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Open Access Research article

Evaluation of 3D-Jury on CASP7 models

László Kaján1* and Leszek Rychlewski12

Author Affiliations

1 BioInfoBank Institute, ul. Limanowskiego 24 A, 60-744 Poznań, Poland

2 Bioinformatics Unit, Department of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614 Poznań, Poland

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BMC Bioinformatics 2007, 8:304  doi:10.1186/1471-2105-8-304

Published: 21 August 2007

Abstract

Background

3D-Jury, the structure prediction consensus method publicly available in the Meta Server http://meta.bioinfo.pl/ webcite, was evaluated using models gathered in the 7th round of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7). 3D-Jury is an automated expert process that generates protein structure meta-predictions from sets of models obtained from partner servers.

Results

The performance of 3D-Jury was analysed for three aspects. First, we examined the correlation between the 3D-Jury score and a model quality measure: the number of correctly predicted residues. The 3D-Jury score was shown to correlate significantly with the number of correctly predicted residues, the correlation is good enough to be used for prediction. 3D-Jury was also found to improve upon the competing servers' choice of the best structure model in most cases. The value of the 3D-Jury score as a generic reliability measure was also examined. We found that the 3D-Jury score separates bad models from good models better than the reliability score of the original server in 27 cases and falls short of it in only 5 cases out of a total of 38. We report the release of a new Meta Server feature: instant 3D-Jury scoring of uploaded user models.

Conclusion

The 3D-Jury score continues to be a good indicator of structural model quality. It also provides a generic reliability score, especially important for models that were not assigned such by the original server. Individual structure modellers can also benefit from the 3D-Jury scoring system by testing their models in the new instant scoring feature http://meta.bioinfo.pl/compare_your_model_example.pl webcite available in the Meta Server.