Virtual Ligand Screening Against Comparative Protein Structure Models

Methods Mol Biol. 2012;819:105-26. doi: 10.1007/978-1-61779-465-0_8.

Abstract

Virtual ligand screening uses computation to discover new ligands of a protein by screening one or more of its structural models against a database of potential ligands. Comparative protein structure modeling extends the applicability of virtual screening beyond the atomic structures determined by X-ray crystallography or NMR spectroscopy. Here, we describe an integrated modeling and docking protocol, combining comparative modeling by MODELLER and virtual ligand screening by DOCK.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Automation
  • Binding Sites
  • Databases, Protein
  • Drug Evaluation, Preclinical / methods*
  • Ligands
  • Models, Molecular*
  • Molecular Sequence Data
  • Proteins / chemistry*
  • Sequence Alignment
  • Structural Homology, Protein*
  • User-Computer Interface*

Substances

  • Ligands
  • Proteins