Journal of Biomolecular NMR

, Volume 63, Issue 2, pp 125–139 | Cite as

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

Article

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-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.

Keywords

Fragment Density functional theory Chemical shift prediction AF-QM/MM NMR 

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.Department of Chemistry and Chemical Biology and BioMaPS InstituteRutgers UniversityPiscatawayUSA
  2. 2.State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational ScienceEast China Normal UniversityShanghaiChina
  3. 3.NYU-ECNU Center for Computational Chemistry at NYU ShanghaiShanghaiChina

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