Method for computing protein binding affinity |
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Authors: | Karney Charles F F Ferrara Jason E Brunner Stephan |
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Affiliation: | Sarnoff Corporation, Princeton, New Jersey 08543-5300, USA. ckarney@sarnoff.com |
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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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Keywords: | free energy binding affinity Monte Carlo methods equilibrium constants proteins |
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