Method for Computing Protein Binding Affinity

Details Method for Computing Protein Binding Affinity Method for Computing Protein Binding Affinity

2004-01-19

arxiv.org/abs/cond-mat/0401348v3

J. Comput. Chem. 26(3), 243-251 (Feb. 2005)

Physics

Condensed Matter

Statistical Mechanics

RevTex, 10 pages with 5 figures. Explanatory figure added

Scientific paper

10.1002/jcc.20167

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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