Method for computing protein binding affinity.
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.
Karney
Charles F F
CF
Sarnoff Corporation, Princeton, New Jersey 08543-5300, USA. ckarney@sarnoff.com
Ferrara
Jason E
JE
Brunner
Stephan
S
D001665:Binding Sites; D003198:Computer Simulation; D008024:Ligands; D008956:Models, Chemical; D009010:Monte Carlo Method; D011485:Protein Binding / Q000502:physiology*; D013816:Thermodynamics
D008024:Ligands