Fig. 12
From: Comparative assessment of strategies to identify similar ligand-binding pockets in proteins
Examples of pocket alignments and the chemical correlation from structure-based virtual screening for proteins selected from the TOUGH-M1 dataset. a-c A Positive pair of spermidine synthase (SPDS) and polyamine receptor SpuE, (d-f) a Negative pair of phosphonoacetaldehyde dehydrogenase PhnY and β-lactamase blaOXA-58. Target structures are aligned according to local alignments reported by (a) APoc and (d) SiteEngine; SPDS, SpuE, PhnY, and blaOXA-58 are colored in salmon, gray, cyan, and yellow, respectively. Cα atoms of binding residues are represented by solid spheres, whereas binding ligands are shown as sticks. Four scatter plots show the correlation of ranks from virtual screening conducted by (b, e) Vina and (c, f) rDock. Each dot represents one library compound, whose ranks against target pockets are displayed on x and y axes. A dashed black line is the diagonal corresponding to a perfect correlation. (b, c) The color and size of dots depend on the Tanimoto coefficient (TC) computed against spermidine that binds to both proteins, SPDS and SpuE, in experimental complex structures; the color scale is displayed on the right