Journal of Computer-Aided Molecular Design

, Volume 11, Issue 5, pp 425–445 | Cite as

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

  • Matthew D. Eldridge
  • Christopher W. Murray
  • Timothy R. Auton
  • Gaia V. Paolini
  • Roger P. Mee


This paper describes the development of a simple empirical scoringfunction designed to estimate the free energy of binding for aprotein–ligand complex when the 3D structure of the complex is knownor can be approximated. The function uses simple contact terms to estimatelipophilic and metal–ligand binding contributions, a simple explicitform for hydrogen bonds and a term which penalises flexibility. Thecoefficients of each term are obtained using a regression based on 82ligand–receptor complexes for which the binding affinity is known. Thefunction reproduces the binding affinity of the complexes with across-validated error of 8.68 kJ/mol. Tests on internal consistency indicatethat the coefficients obtained are stable to changes in the composition ofthe training set. The function is also tested on two test sets containing afurther 20 and 10 complexes, respectively. The deficiencies of this type offunction are discussed and it is compared to approaches by other workers.

Binding affinity prediction Empirical scoring function De novo molecular design Protein–ligand complexes 


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Copyright information

© Kluwer Academic Publishers 1997

Authors and Affiliations

  • Matthew D. Eldridge
    • 1
  • Christopher W. Murray
    • 1
  • Timothy R. Auton
    • 1
  • Gaia V. Paolini
    • 1
  • Roger P. Mee
    • 1
  1. 1.Proteus Molecular Design Ltd., Proteus HouseMacclesfield, CheshireU.K.

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