Molecular Docking

  • Garrett M. Morris
  • Marguerita Lim-Wilby
Part of the Methods Molecular Biology™ book series (MIMB, volume 443)


Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand—protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.


AutoDock Computer-assisted drug design DOCK FlexX GOLD ICM Molecular recognition Protein—ligand docking 



This manuscript is TSRI publication number 18829. This work was supported by the National Institutes of Health (NIH) grant R01-GM069832.


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Garrett M. Morris
    • 1
  • Marguerita Lim-Wilby
    • 2
  1. 1.Department of Molecular BiologyThe Scripps Research InstituteLa JollaUSA
  2. 2.BioSolveIT GmbHSankt AugustinGermany

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