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.
CITATION STYLE
Anighoro, A., & Bajorath, J. (2018). A hybrid virtual screening protocol based on binding mode similarity. In Methods in Molecular Biology (Vol. 1824, pp. 165–176). Humana Press Inc. https://doi.org/10.1007/978-1-4939-8630-9_9
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