Method for Computing Protein Binding Affinity

2004/01/31 by Charles F. F. Karney, Jason E. Ferrara, Stephan Brunner
Physics and Astronomy · Biochemistry, Genetics and Molecular Biology · #cond-mat.stat-mech #physics.bio-ph #physics.chem-ph #q-bio.QM

paper · pdf · doi:10.1002/jcc.20167

published as J. Comput. Chem. 26(3), 243-251 (Feb. 2005) · RevTex, 10 pages with 5 figures. Explanatory figure added

arxiv created 2004/09/09 · arxiv updated 2009/12/01

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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