Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets
Citations Over TimeTop 1% of 2007 papers
Abstract
Virtual screening by molecular docking has become a widely used approach to lead discovery in the pharmaceutical industry when a high-resolution structure of the biological target of interest is available. The performance of three widely used docking programs (Glide, GOLD, and DOCK) for virtual database screening is studied when they are applied to the same protein target and ligand set. Comparisons of the docking programs and scoring functions using a large and diverse data set of pharmaceutically interesting targets and active compounds are carried out. We focus on the problem of docking and scoring flexible compounds which are sterically capable of docking into a rigid conformation of the receptor. The Glide XP methodology is shown to consistently yield enrichments superior to the two alternative methods, while GOLD outperforms DOCK on average. The study also shows that docking into multiple receptor structures can decrease the docking error in screening a diverse set of active compounds.
Related Papers
- → Computational protein–ligand docking and virtual drug screening with the AutoDock suite(2016)2,604 cited
- → CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting(2022)1,538 cited
- → Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases(2004)413 cited
- → Q‐Dock: Low‐resolution flexible ligand docking with pocket‐specific threading restraints(2008)55 cited
- Molecular Docking Technique(2021)