AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.

ABSTRACT: We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson-Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF

SUBMITTER: Swails J 

PROVIDER: S-EPMC6556433 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature