Evaluation of 3D-Jury on CASP7 models
<p>Abstract</p> <p>Background</p> <p>3D-Jury, the structure prediction consensus method publicly available in the Meta Server <url>http://meta.bioinfo.pl/</url>, was evaluated using models gathered in the 7<sup><it>th </it></sup>round...
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| Format: | Article |
| Language: | English |
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BMC
2007-08-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/8/304 |
| _version_ | 1819053425332060160 |
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| author | Rychlewski Leszek Kaján László |
| author_facet | Rychlewski Leszek Kaján László |
| author_sort | Rychlewski Leszek |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>3D-Jury, the structure prediction consensus method publicly available in the Meta Server <url>http://meta.bioinfo.pl/</url>, was evaluated using models gathered in the 7<sup><it>th </it></sup>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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 <url>http://meta.bioinfo.pl/compare_your_model_example.pl</url> available in the Meta Server.</p> |
| first_indexed | 2024-12-21T12:35:31Z |
| format | Article |
| id | doaj.art-622696ec68c44ed993b51e519d7bdb17 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-21T12:35:31Z |
| publishDate | 2007-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-622696ec68c44ed993b51e519d7bdb172022-12-21T19:03:55ZengBMCBMC Bioinformatics1471-21052007-08-018130410.1186/1471-2105-8-304Evaluation of 3D-Jury on CASP7 modelsRychlewski LeszekKaján László<p>Abstract</p> <p>Background</p> <p>3D-Jury, the structure prediction consensus method publicly available in the Meta Server <url>http://meta.bioinfo.pl/</url>, was evaluated using models gathered in the 7<sup><it>th </it></sup>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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 <url>http://meta.bioinfo.pl/compare_your_model_example.pl</url> available in the Meta Server.</p>http://www.biomedcentral.com/1471-2105/8/304 |
| spellingShingle | Rychlewski Leszek Kaján László Evaluation of 3D-Jury on CASP7 models BMC Bioinformatics |
| title | Evaluation of 3D-Jury on CASP7 models |
| title_full | Evaluation of 3D-Jury on CASP7 models |
| title_fullStr | Evaluation of 3D-Jury on CASP7 models |
| title_full_unstemmed | Evaluation of 3D-Jury on CASP7 models |
| title_short | Evaluation of 3D-Jury on CASP7 models |
| title_sort | evaluation of 3d jury on casp7 models |
| url | http://www.biomedcentral.com/1471-2105/8/304 |
| work_keys_str_mv | AT rychlewskileszek evaluationof3djuryoncasp7models AT kajanlaszlo evaluationof3djuryoncasp7models |