Structure-Based Virtual Screening

Methods Mol Biol. 2017:1558:111-124. doi: 10.1007/978-1-4939-6783-4_5.

Abstract

Structure-based virtual screening (SBVS) is a computational approach used in the early-stage drug discovery campaign to search a chemical compound library for novel bioactive molecules against a certain drug target. It utilizes the three-dimensional (3D) structure of the biological target, obtained from X-ray, NMR, or computational modeling, to dock a collection of chemical compounds into the binding site and select a subset of these compounds based on the predicted binding scores for further biological evaluation. In the present work, we illustrate the basic process of conducting a SBVS with examples using freely accessible tools and resources.

Keywords: AutoDock Vina; Drug discovery; Molecular docking; OpenBabel; UCSF Chimera; Virtual screening.

MeSH terms

  • Binding Sites
  • Computer Simulation*
  • Drug Discovery / methods*
  • Drug Evaluation, Preclinical / methods*
  • Ligands
  • Models, Molecular*
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Protein Binding
  • Protein Conformation
  • Quantitative Structure-Activity Relationship*
  • Small Molecule Libraries
  • Software*
  • User-Computer Interface
  • Web Browser
  • Workflow

Substances

  • Ligands
  • Small Molecule Libraries