UNASSIGNED: Representative pairs of @entity3689 side chains and nucleic acid bases extracted from available high-quality structures of protein-DNA complexes were analyzed using a range of computational methods. CCSD(T)/CBS interaction energies were calculated for the chosen 272 pairs. These reference interaction energies were used to test the @entity4885 .5/CBS, @entity4885 .X/CBS, @entity4885 -F12, DFT-D3, PM6, and Amber force field methods. Method @entity4885 .5 provided excellent agreement with reference data (root-mean-square error (RMSE) of 0.11 kcal/mol), which is more than 1 order of magnitude faster than the CCSD(T) method. When @entity4885 -F12 and @entity4885 .5 were combined, the results were within reasonable accuracy (0.20 kcal/mol), with a computational savings of almost 2 orders of magnitude. Therefore, this method is a promising tool for accurate calculations of interaction energies in protein-DNA motifs of up to    100 atoms, for which CCSD(T)/CBS benchmark calculations are not feasible. B3- @entity5812 -D3 calculated with def2-TZVPP and def2-QZVP basis sets yielded sufficiently good results with a reasonably small RMSE. This method provided better results for neutral systems, whereas positively charged species exhibited the worst agreement with the benchmark data. The Amber force field yielded unbalanced results-performing well for systems containing nonpolar @entity3534 but severely underestimating interaction energies for charged complexes. The semiempirical PM6 method with corrections for @entity3884 bonding and dispersion energy (PM6-D3H4) exhibited considerably smaller error than the Amber force field, which makes it an effective tool for modeling extended protein-ligand complexes (of up to 10   000 atoms).

Representative XXXX Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems.

@entity3534 :: ('MESH:D000596', 'Chemical') :: ['amino acids'] @entity3884 :: ('MESH:D006859', 'Chemical') :: ['hydrogen'] @entity4885 :: ('100129339', 'Gene') :: ['MP2'] @entity5812 :: ('26191', 'Gene') :: ['LYP'] @entity3689 :: ('D000596', 'Chemical') :: ['amino acid']
@entity3689 :: (D000596,Chemical) :: ['Amino Acid']
