A Hybrid Virtual Screening Protocol Based on Binding Mode Similarity.
In structure-based virtual screening (SBVS), a scoring function is usually applied to rank a database of docked compounds. Docking programs are often successful in reproducing experimental binding modes; however, the estimation of binding affinity still is the Achilles' heel of docking. The integration of SB and ligand-based (LB) methods is considered a promising strategy to increase hit rates in VS. Herein, we describe a hybrid protocol that is based on the assessment of binding mode similarity between docked compounds and a bound reference ligand. In this context, both experimental and computationally modeled poses have been successfully used as references for three-dimensional (3D) similarity calculations. In this chapter, the methods applied in recent validation studies are described.
['Anighoro|Andrew|A|', 'Bajorath|Jürgen|J|']
D062105:Molecular Docking Simulation D012984:Software
Virtual screening Binding mode 3D similarity Compound ranking Homology modeling Molecular docking Protein–ligand interaction fingerprints