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The effect of multiple binding modes on empirical modeling of ligand docking to proteins

Published online by Cambridge University Press:  01 May 1999

RACHEL BREM
Affiliation:
Department of Pharmaceutical Chemistry, Box 1204, University of California at San Francisco, San Francisco, California 94143-1204 Graduate Group in Biophysics, Box 0448, University of California at San Francisco, San Francisco, California 94143-1204
KEN A. DILL
Affiliation:
Department of Pharmaceutical Chemistry, Box 1204, University of California at San Francisco, San Francisco, California 94143-1204
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Abstract

A popular approach to the computational modeling of ligand/receptor interactions is to use an empirical free energy like model with adjustable parameters. Parameters are learned from one set of complexes, then used to predict another set. To improve these empirical methods requires an independent way to study their inherent errors. We introduce a toy model of ligand/receptor binding as a workbench for testing such errors. We study the errors incurred from the two state binding assumption—the assumption that a ligand is either bound in one orientation, or unbound. We find that the two state assumption can cause large errors in free energy predictions, but it does not affect rank order predictions significantly. We show that fitting parameters using data from high affinity ligands can reduce two state errors; so can using more physical models that do not use the two state assumption. We also find that when using two state models to predict free energies, errors are more severe on high affinity ligands than low affinity ligands. And we show that two state errors can be diagnosed by systematically adding new binding modes when predicting free energies: if predictions worsen as the modes are added, then the two state assumption in the fitting step may be at fault.

Type
Research Article
Copyright
1999 The Protein Society

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