Limits of Free Energy Computation for Protein-Ligand Interactions.

ABSTRACT: A detailed error analysis is presented for the computation of protein-ligand interaction energies. In particular, we show that it is probable that even highly accurate computed binding free energies have errors that represent a large percentage of the target free energies of binding. This is due to the observation that the error for computed energies quasi-linearly increases with the increasing number of interactions present in a protein-ligand complex. This principle is expected to hold true for any system that involves an ever increasing number of inter or intra-molecular interactions (e.g. ab initio protein folding). We introduce the concept of best-case scenario errors (BCS(errors)) that can be routinely applied to docking and scoring exercises and used to provide errors bars for the c

SUBMITTER: Merz KM 

PROVIDER: S-EPMC2866028 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature