Journal: PLoS Computational Biology

Article Title: A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

doi: 10.1371/journal.pcbi.1006483

Figure Lengend Snippet: A-C) The ROC curves for residue- (A), surface- (B), and interaction-based (C) comparison methods. The name of the tool is colored according to its corresponding ROC curve. The binding site comparison tools are sorted in descending order with respect to the AUC. Thin lines represent the resulting ROC curve for the scoring scheme that yielded the highest AUC. (A) A slightly higher AUC for SiteAlign was obtained if distance d2 was applied for binding site pair ranking. (B) For the surface-based methods, the Tanimoto (color) for Shaper or VolSite/Shaper and the ColorTanimoto for SiteHopper led to the highest AUC. (C) The use of the Tanimoto coefficient as similarity measure led to the highest AUC for TIFP(PDB). D-F) EFs for residue- (D), surface- (E), and interaction-based (F) comparison methods. A linear color gradient ranging from white for the highest value to gray to black for the lowest value was applied for the EFs at different percentages of screened data set.

Article Snippet: The AUC values for the resulting ROC curves were also calculated using KNIME.

Techniques: Residue, Comparison, Binding Assay

Journal: PLoS Computational Biology

Article Title: A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

doi: 10.1371/journal.pcbi.1006483

Figure Lengend Snippet: A-C) The ROC curves for residue- (A), surface- (B), and interaction-based (C) comparison methods. The name of the tool is colored according to its corresponding ROC curve. The binding site comparison tools are sorted in descending order with respect to the AUC. (A) The highest AUC was obtained for SiteAlign when using distance d1. (B) All Shaper comparisons led to higher AUCs for the scoring measure Tanimoto (color). SiteEngine results slightly improved the AUC for the distance scoring scheme. D-F) EFs for residue- (D), surface- (E), and interaction-based (F) comparison methods. A linear color gradient ranging from white for the highest value to gray to black for the lowest value was applied for the EFs at different percentages of screened data set.

Article Snippet: The AUC values for the resulting ROC curves were also calculated using KNIME.

Techniques: Residue, Comparison, Binding Assay

Journal: PLoS Computational Biology

Article Title: A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

doi: 10.1371/journal.pcbi.1006483

Figure Lengend Snippet: A-C) The ROC curves for residue- (A), surface- (B), and interaction-based (C) comparison methods. The name of the tool is colored according to its corresponding ROC curve. The binding site comparison tools are sorted in descending order with respect to their AUC. (A) PocketMatch showed the best AUC for the score PMScore min (thin orange line). (B) The scores SVA, RefTversky (color), RefTversky (color), RefTversky (color), RefTversky (color), and ColorTanimoto led to the highest AUC values for ProBiS, Shaper, Shaper(PDB), VolSite/Shaper, VolSite/Shaper(PDB), and SiteHopper, respectively (thin lines). (C) The highest AUC was obtained for IsoMIF and TIFP(PDB) when using taniM and the Tanimoto coefficient as similarity measure (thin lines). D-F) EFs for residue- (D), surface- (E), and interaction-based (F) comparison methods. A linear color gradient ranging from white for the highest value to gray to black for the lowest value was applied for the EFs at different percentages of screened data set.

Article Snippet: The AUC values for the resulting ROC curves were also calculated using KNIME.

Techniques: Residue, Comparison, Binding Assay

Journal: PLoS Computational Biology

Article Title: A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

doi: 10.1371/journal.pcbi.1006483

Figure Lengend Snippet: A-C) The ROC curves for residue- (A), surface- (B), and interaction-based (C) comparison methods. The name of the tool is colored according to its corresponding ROC curve. The binding site comparison tools are sorted in descending order with respect to their AUC. (A) PocketMatch showed the best AUC for the score PMScore min (thin orange line). (B) The scores SVA, Tanimoto (color), Tanimoto (color), RefTversky (color), RefTversky (color), and ColorTanimoto led to the highest AUC values for ProBiS, Shaper, Shaper(PDB), VolSite/Shaper, VolSite/Shaper(PDB), and SiteHopper, respectively (thin lines). (C) The highest AUC was obtained for TIFP(PDB) when using the Tanimoto coefficient as scoring measure (thin dark green line). D-F) EFs for residue- (D), surface- (E), and interaction-based (F) comparison methods. A linear color gradient ranging from white for the highest value to gray to black for the lowest value was applied for the EFs at different percentages of screened data set.

Article Snippet: The AUC values for the resulting ROC curves were also calculated using KNIME.

Techniques: Residue, Comparison, Binding Assay

Journal: PLoS Computational Biology

Article Title: A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

doi: 10.1371/journal.pcbi.1006483

Figure Lengend Snippet: A-C) The ROC curves for residue- (A), surface- (B), and interaction-based (C) comparison methods. The name of the tool is colored according to its corresponding ROC curve. The binding site comparison tools are sorted in descending order with respect to the AUC. (A) The best AUC for SiteAlign resulted from the d1 distance (thin red line). (B) For ProBiS, VolSite/Shaper, SiteEngine, and SiteHopper the scores SVA, Tanimoto (color), TotalScore, and ShapeTanimoto yielded the best AUC values (thin lines). (C) For TIFP(PDB), the use of the Hamming distance led to the best results with respect to AUC (thin line). D-F) EFs for residue- (D), surface- (E), and interaction-based (F) comparison methods. A linear color gradient ranging from white for the highest value to gray to black for the lowest value was applied for the EFs at different percentages of screened data set.

Article Snippet: The AUC values for the resulting ROC curves were also calculated using KNIME.

Techniques: Residue, Comparison, Binding Assay

Journal: PLoS Computational Biology

Article Title: A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

doi: 10.1371/journal.pcbi.1006483

Figure Lengend Snippet: A-C) The ROC curves for residue- (A), surface- (B), and interaction-based (C) comparison methods. The name of the tool is colored according to its corresponding ROC curve. The binding site comparison tools are sorted in descending order with respect to the AUC. (A) The thin red line represents the resulting ROC curve for SiteAlign when using the distance d1. (B) Thin lines represent the ROC curves for ProBiS, Shaper, Shaper(PDB), VolSite/Shaper, VolSite/Shaper(PDB), SiteEngine and SiteHopper when using the scoring schemes SVA, FitTversky (color), FitTversky (color), RefTversky (color), Tanimoto (fit), distance, and ShapeTanimoto, respectively. (C) The thin line represents the resulting ROC curve for IsoMIF and the taniMW score. D-F) EFs for residue- (D), surface- (E), and interaction-based (F) comparison methods. A linear color gradient ranging from white for the highest value to gray to black for the lowest value was applied for the EFs at different percentages of screened data set.

Article Snippet: The AUC values for the resulting ROC curves were also calculated using KNIME.

Techniques: Residue, Comparison, Binding Assay

Journal: PLoS Computational Biology

Article Title: A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

doi: 10.1371/journal.pcbi.1006483

Figure Lengend Snippet: A-C) The ROC curves for residue- (A), surface- (B), and interaction-based (C) comparison methods. The name of the tool is colored according to its corresponding ROC curve. The binding site comparison tools are sorted in descending order with respect to the AUC. (A) SiteAlign yielded a slightly better AUC if the distance d1 was used (thin line). (B) The best AUC values for ProBis, Shaper, Shaper(PDB), VolSite/Shaper, VolSite/Shaper(PDB), SiteEngine, and SiteHopper resulted from the scoring measures Zscore, Tanimoto (color), Tanimoto (color), Tanimoto (color), Tanimoto (color), TotalScore, and ShapeTanimoto, respectively (thin lines). D-F) EFs for residue- (D), surface- (E), and interaction-based (F) comparison methods. A linear color gradient ranging from white for the highest value to gray to black for the lowest value was applied for the EFs at different percentages of screened data set.

Article Snippet: The AUC values for the resulting ROC curves were also calculated using KNIME.

Techniques: Residue, Comparison, Binding Assay