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Glycoinformatics

Volume 1273 of the series Methods in Molecular Biology pp 467-474

Date:

Scoring Functions for AutoDock

  • Anthony D. HillAffiliated withSt. Jude Medical
  • , Peter J. ReillyAffiliated withDepartment of Chemical and Biological Engineering, Iowa State University Email author 

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Abstract

Automated docking allows rapid screening of protein–ligand interactions. A scoring function composed of a force field and linear weights can be used to compute a binding energy from a docked atom configuration. For different force fields or types of molecules, it may be necessary to train a custom scoring function. This chapter describes the data and methods one must consider in developing a custom scoring function for use with AutoDock.

Key words

AutoDock Automated docking Gibbs free energies of binding Protein–ligand complexes Scoring functions