Table 3. Quality Criteria for the Selection of Training Set Structures I–III^a.

- X-ray structure with crystallographic resolution ≤2.5 Å

- successful match of ligand topology (best Proasis2 ligand quality)

- only noncovalent binding between ligand and protein*

- no symmetry contacts*

- no alternative conformations*

- no clashes*

- no missing atoms*

- no broken residues*

- minimum occupancy = 1.0*

- minimum real space correlation coefficient ≥ 0.7*

- ligand strain energy ≤ 8 kcal/mol

- ligands from medicinal chemistry programs

- binding data available (Ki, Kd, IC50) and measured with same assay

^aPoints marked with ∗ apply only to protein–ligand contact atoms within a distance threshold of 5.0 Å.