Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation

J Comput Aided Mol Des. 2009 Aug;23(8):541-54. doi: 10.1007/s10822-009-9268-1. Epub 2009 May 7.


We have developed a method that uses energetic analysis of structure-based fragment docking to elucidate key features for molecular recognition. This hybrid ligand- and structure-based methodology uses an atomic breakdown of the energy terms from the Glide XP scoring function to locate key pharmacophoric features from the docked fragments. First, we show that Glide accurately docks fragments, producing a root mean squared deviation (RMSD) of <1.0 A for the top scoring pose to the native crystal structure. We then describe fragment-specific docking settings developed to generate poses that explore every pocket of a binding site while maintaining the docking accuracy of the top scoring pose. Next, we describe how the energy terms from the Glide XP scoring function are mapped onto pharmacophore sites from the docked fragments in order to rank their importance for binding. Using this energetic analysis we show that the most energetically favorable pharmacophore sites are consistent with features from known tight binding compounds. Finally, we describe a method to use the energetically selected sites from fragment docking to develop a pharmacophore hypothesis that can be used in virtual database screening to retrieve diverse compounds. We find that this method produces viable hypotheses that are consistent with known active compounds. In addition to retrieving diverse compounds that are not biased by the co-crystallized ligand, the method is able to recover known active compounds from a database screen, with an average enrichment of 8.1 in the top 1% of the database.

MeSH terms

  • Algorithms
  • Binding Sites
  • Computer-Aided Design
  • Drug Discovery*
  • Humans
  • Ligands*
  • Protein Binding
  • Protein Conformation
  • Proteins / chemistry*
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / therapeutic use
  • Software
  • Structure-Activity Relationship
  • Thermodynamics


  • Ligands
  • Proteins
  • Small Molecule Libraries