Protein Function Prediction by Daisuke Kihara

Author:Daisuke Kihara
Language: eng
Format: epub
Publisher: Springer New York, New York, NY

Target/off-target

Global similarity

Local similarity

Sequence identity (%)

TM-score

Pocket RMSD (Å)

Ligand RMSD (Å)

BFD/OXC

25

0.85

3.18

0.88

BFD/hE1b

25

0.35

2.72

0.89

eMatchSite requires binding sites and residues to be annotated by eFindSite; therefore, eFindSite webserver at http://​www.​brylinski.​org/​efindsite was used to identify binding sites in the crystal structures of BFD, OXC, and hE1b. The results are shown in Fig. 3. A binding site for ThTDP in the primary target BFD was identified with a 95% confidence; the Matthews correlation coefficient (MCC) calculated over binding residues is as high as 0.89 (Fig. 3a). The prediction confidence for off-targets OXC and hE1b is 94% and 93%, respectively. MCC calculated for binding residues identified in OXC is 0.78 (Fig. 3b) and 0.88 for hE1b (Fig. 3c). Note that bound ThTDP ligands are shown in Fig. 3 only to assess the accuracy of binding pocket prediction with eFindSite, which detects and annotates binding sites in ligand-free protein structures [14, 15].

Fig. 3Ligand binding pockets annotated with eFindSite. Target structures are shown as transparent gray cartoons, whereas binding residues are rendered as the molecular surface for (a) BFD, (b) OXC, and (c) hE1b. Binding sites in BFD, OXC, and hE1b are colored in orange, pink, and cyan, respectively. ThTDP ligands bound to the target structures are shown as sticks colored by the atom type (carbon—green, nitrogen—blue, oxygen—red, sulfur—yellow, phosphorus—tan)

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