Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes.

ABSTRACT: A largely unsolved problem in computational biochemistry is the accurate prediction of binding affinities of small ligands to protein receptors. We present a detailed analysis of the systematic and random errors present in computational methods through the use of error probability density functions, specifically for computed interaction energies between chemical fragments comprising a protein-ligand complex. An HIV-II protease crystal structure with a bound ligand (indinavir) was chosen as a model protein-ligand complex. The complex was decomposed into twenty-one (21) interacting fragment pairs, which were studied using a number of computational methods. The chemically accurate complete basis set coupled cluster theory (CCSD(T)/CBS) interaction energies were used as reference values to gen

SUBMITTER: Faver JC 

PROVIDER: S-EPMC3110077 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature