Automated prediction of ligand-binding sites in proteins

Rodney Harris, Arthur J. Olson, David S. Goodsell

Research output: Contribution to journalArticlepeer-review

105 Scopus citations


We present a method, termed AutoLigand, for the prediction of ligand-binding sites in proteins of known structure. The method searches the space surrounding the protein and finds the contiguous envelope with the specified volume of atoms, which has the largest possible interaction energy with the protein. It uses a full atomic representation, with atom types for carbon, hydrogen, oxygen, nitrogen and sulfur (and others, if desired), and is designed to minimize the need for artificial geometry. Testing on a set of 187 diverse protein-ligand complexes has shown that the method is successful in predicting the location and approximate volume of the binding site in 73% of cases. Additional testing was performed on a set of 96 protein-ligand complexes with crystallographic structures of apo and holo forms, and AutoLigand was able to predict the binding site in 80% of the apo structures.

Original languageEnglish (US)
Pages (from-to)1506-1517
Number of pages12
JournalProteins: Structure, Function and Genetics
Issue number4
StatePublished - Mar 2008
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology


  • Autodock
  • Functionalsiteprediction
  • Rational drug design
  • Structural genomics


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