Performance of the method considering first-ranked predictions.

<p>Complete results, as percentage of analyzed protein structures in which the method places a correct prediction in the first rank for the three types of nucleotide modules. Each nucleotide type is represented by a doughnut chart that is divided in three sectors, one for each nucleotide module (blue for the nucleobase, red for the carbohydrate and green for the phosphate). The size of each module sector is proportional to the percentage of proteins in which the method is successful. The columns divide the nucleotides by their architecture type: NCP stands for nucleobase-carbohydrate-phosphate (e.g. the AMP) and so on. Moreover nucleotides are grouped by their characteristic molecular feature so that rows divide them in guanine-, adenine-, flavin- and nicotinamide-containing nucleotides.</p

Results of the method after ranking predictions considering the nucleotide type.

<p>Complete results for the sc-PDB dataset divided by nucleotide type, as percentage of analyzed protein structures in which the method places a correct prediction in the first, top three, top five and top ten predictions for the three types of nucleotide modules.</p

F-score of the method at different R.M.S.D. thresholds.

<p>Average F-scores of the method (considering all the nucleotide types) for each nucleotide module and for each R.M.S.D. threshold used during the structural comparison step.</p

F-scores measuring the method performance for the different nucleotides.

<p>Complete results reporting the F-scores for all the nucleotide types and for each nucleotide module considered. The bars are colored depending on the nucleotide module: blue for the nucleobase, red for the carbohydrate and green for the phosphate.</p

Minimum and maximum distances allowed between nucleotide modules.

<p>These distances (in Ångström) are calculated between the centroids of nucleotide modules.</p

Comparison with another method for the prediction if nucleotide-bingind sites.

<p>Comparison between the method developed by Saito <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050240#pone.0050240-Saito1" target="_blank">[17]</a> and the methodology presented in this work. The first group of bars on the left represents the performance of Saito’s method. The other groups of bars represent the performance of our method for the different nucleotide modules. Bars are colored depending on the protein dataset: proteins binding adenine- (blue), guanine- (red) nicotinamide- (green) and flavin-containing (purple) nucleotides.</p

Performance of the method on protein homology models.

<p>The performance of the method (Y axis), measured as the percentage of protein structures in which the first-ranked prediction correctly identifies the true nucleotide-binding site, plotted as a function of the GDT value (X axis) of the homology-models.</p

Minimum distance allowed for nucleotide modules from the protein surface.

<p>Minimum distance, in Ångström, allowed for a predicted nucleotide module from the solvent excluded surface. The distance is calculated considering any atom of the nucleotide module and any vertex of the mesh representing the solvent excluded surface.</p

Overall results of the method after ranking predictions.

<p>Complete results, as percentages of analyzed protein structures in which the method places a correct prediction of the three types of nucleotide modules considering the 1, 3, 5 and 10 top ranks.</p

Comparison of the method performance on apo and holo structures.

<p>Complete results for the LigASite dataset (apo-holo structures), as percentage of analyzed protein structures in which the method places a correct prediction in the first, top three, top five and top ten predictions for the three types of nucleotide modules.</p