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  • Title: Method for computing protein binding affinity.
    Author: Karney CF, Ferrara JE, Brunner S.
    Journal: J Comput Chem; 2005 Feb; 26(3):243-51. PubMed ID: 15614799.
    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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