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Method for computing protein binding affinity
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DOI：10.1002/jcc.20167.png)
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Abstract
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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. (C) 2004 Wiley Periodicals, Inc.
Keywords:
free energy
binding affinity
Monte Carlo methods
equilibrium constants
proteins
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