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Open Access Research article

ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification

Vichetra Sam1, Chin-Hsien Tai2, Jean Garnier13, Jean-Francois Gibrat3, Byungkook Lee2 and Peter J Munson1*

Author Affiliations

1 Mathematical and Statistical Computing Laboratory, DCB, CIT, NIH, DHHS, Bethesda, MD, USA

2 Laboratory of Molecular Biology, CCR, NCI, NIH, DHHS, Bethesda, MD, USA

3 Mathematique Informatique et Genome, INRA, Jouy-en-Josas, France

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BMC Bioinformatics 2006, 7:206  doi:10.1186/1471-2105-7-206

Published: 13 April 2006

Additional files

Additional File 1:

• VAST and SHEBA heat maps • Complete heat map of VAST and SHEBA, obtained for a Pcli cutoff value of 2.5 and a Zscore cutoff value of 2.7, respectively. The cutoffs correspond to an overall average FPR of 0.01, and result in an overall average TPR of 0.616 and 0.748 for VAST and SHEBA respectively. The x (target folds) and y (query folds) axes of the heat maps are labeled by the SCOP folds, grouped into the different classes A, B, C, D, E, F and G. Each pixel within the heat maps represents a fold-specific true or false positive rate and takes value between 0 and 1. Diagonal and off-diagonal pixels correspond to fold-specific true positive rate TPRi(c) (eq. 4, see Methods) and fold-specific false positive rate FPRi,j(c) (eq. 3, see Methods) respectively.

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Additional File 2:

• Fold-specific True Positive Rates (see Methods) at 1% False Positive Rate, for VAST and SHEBA, for 468 SCOP Folds in the order of the Heat Map. • Rows 1 to 7 correspond respectively to: the row number, the SCOP fold identifier, the number of domains within a fold, TPRi value obtained by the fold with VAST, TPRi value obtained by the fold with SHEBA, SCOP name of the fold, and SCOP description of the fold.

Format: PDF Size: 165KB Download file

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Open Data