Good ligand pose
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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