Figure 1

Determination of knowledge-based potentials for a template's active site. In order to illustrate the determination of potentials, 10 3D models were created for homologs of TrpF and superimposed (left panel). The right panel shows the 3D position of groups (the various sets HB_Set _i ) forming hydrogen bonds with the ligand rCdRP, which is plotted in green. The geometry of resulting scatter-plots was utilized to determine for each residue a knowledge-based potential; see Methods for details. Color code: (Arg, His, Lys), blue; (Asp, Glu), red; (Asn, Cys, Gln, Ser, Thr, Tyr), yellow. Hydrophobic residues are plotted in grey. Plots were generated by using SWISS-MODEL.