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Method for Computing Protein Binding Affinity | | Charles F. F. Karney
; Jason E. Ferrara
; Stephan Brunner
; | | Date: |
19 Dec 2003 | | Journal: | J. Comput. Chem. 26(3), 243-251 (Feb. 2005) DOI: 10.1002/jcc.20167 | | Subject: | Statistical Mechanics; Chemical Physics; Biological Physics; Quantitative Methods | cond-mat.stat-mech physics.bio-ph physics.chem-ph q-bio.QM | | Affiliation: | Sarnoff Corporation, Locus Pharmaceuticals | | 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. | | Source: | arXiv, cond-mat/0401348 | | Services: | Forum | Review | PDF | Favorites | |
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