Good ligand pose: Difference between revisions

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Latest revision as of 20:25, 8 October 2012

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