title: 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-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.
authors.affiliation: Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Swails
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China.
authors.forename: Tong
authors.initials: T
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China. xiaohe@phy.ecnu.edu.cn.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China. xiaohe@phy.ecnu.edu.cn.
authors.forename: Xiao
authors.initials: X
authors.lastname: He
authors.affiliation: Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA. case@biomaps.rutgers.edu.
authors.forename: David A
authors.initials: DA
authors.lastname: Case
mesh_terms: D004247:DNA / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D009696:Nucleic Acids / Q000737:chemistry*; D009711:Nucleotides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry
chemical_list: D009696:Nucleic Acids; D009711:Nucleotides; D011506:Proteins; D012997:Solvents; D004247:DNA
keywords: AF-QM/MM NMR; Chemical shift prediction; Density functional theory; Fragment