Good ligand pose

What makes a good ligand pose? You can see for yourself by examinging the experimentally observed poses of ligands in the protein data bank (aka PDB).

When reviewing hits from a docking screen, here are the features we look for:

good features

• overall good shape complementarity
• good polar matches between ligand and protein
• good apolar matches between ligand and protein
• not too floppy

bad features

• dangle polarity into solvent (bad because part of the ligand is being "wasted")
• polar to apolar matchups between ligand and protein
• failure to use features of ligand or protein in binding site
• too floppy

problems specific to dock3.5.54 (and thus DOCK Blaster)

• bad conformation ("internal clashes")
• bad tautomer or protonation choice
• broken molecule