Fig. 7
From: Comparative assessment of strategies to identify similar ligand-binding pockets in proteins
Examples of local alignments constructed by pocket matching algorithms for a pair of structurally dissimilar ATP/ADP-binding proteins in the APoc dataset. Inositol 1,4,5-trisphosphate 3-kinase B [IP(3)-3 KB, violet] is aligned to glutathione synthetase (GSHase, green). a The reference alignment obtained by the superposition of bound ligands is compared to pocket alignments by (b) G-LoSA and (c) APoc. Cα atoms of binding residues are represented by solid spheres, whereas adenine nucleotides are shown as solid sticks. (d-g) Textual pocket alignments between IP(3)-3 KB and GSHase, (d↔e) the reference alignment and those constructed by (d↔f) G-LoSA and (d↔g) APoc. Each box represents a binding residue. Alignments are sorted by the sequence order of IP(3)-3 KB in (d) (violet). Equivalent residues in Ipk2 are colored in green in (e), whereas in (f) and (g), correctly aligned residues with respect to the reference alignment are colored in yellow and misaligned residues are colored in red. Alignment positions reversing the sequence order are marked by asterisks