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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Method for computing protein binding affinity
Charles F F Karney1, Jason E Ferrara, Stephan Brunner
1Sarnoff Corporation, Princeton, New Jersey 08543-5300, USA. ckarney@sarnoff.com
Abstract:
A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move, which allows transitions between the unbound and bound states. Provided that an accurate protein structure is given, that the protein-ligand binding site is known, and that an accurate chemical force field together with a continuum solvation model is used, this method provides a quantitative estimate of the free energy of binding.
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