title: Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping.
abstract: BACKGROUND
  Two recent technological advances dramatically reducing the rate of false-negatives in activity prediction by docking flexible 3D models of compounds include multi-conformational docking (mPockDock) and the docking of candidates to atomic property fields derived by co-crystallized ligands (mApfDock).
  
  
  RESULTS
  The mApfDock and mPockDock provide the AUC of 90.4 and 83.8%, respectively. The mApfDock gave better performance when compounds required large induced-fit pocket changes unseen in crystallography, whereas the mPockDock is superior when the co-crystallized ligands do not represent sufficient chemical and binding location diversity.
  
  
  CONCLUSIONS
  Both approaches proved to be efficient for scaffold hopping; they are complementary when the coverage of the co-crystallized complexes is poor but become convergent when the complexes are diverse enough.
authors.affiliation: Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Yu-Chen
authors.initials: YC
authors.lastname: Chen
authors.forename: Max
authors.initials: M
authors.lastname: Totrov
authors.forename: Ruben
authors.initials: R
authors.lastname: Abagyan
mesh_terms: D000818:Animals; D002626:Chemistry, Pharmaceutical; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation
chemical_list: D008024:Ligands