Figure 5

FIGURE 5. Multiple ligands alignment within 3D field potential.
Several biochemically validated ligands were used to construct the field potential. The 2D MOL models were minimized in the OPLS force field, and aligned in three-dimensional space against physico-chemical field potential generated from their structures. The alignment superimposes common chemical features. The superimpositions reflects the ligand features beneficial for protein target binding, even if target itself is not known. Note, that the core structure (optimal ligand scaffold) can be easily deduced from the alignment.

Figure 5