Estimating chemical shifts in proteins and nucleic acids

SHIFTS takes a protein structure in Brookhaven (PDB) format, and computes proton chemical shifts from empirical formulas. It can also compute N, Cα, Cβ and C' shifts in proteins, using a database based on DFT calculations on peptides. It also provides an "afnmr" (Automated Fragemention approach for NMR) to compute chemical shifts and anisotropies in biomolecules.

Starting in Oct. 2018, we are also packaging up the afnmr functionality in a separate package, which is self-contained and does not require AmberTools. See below for more information. (Note: this package contains the most up-to-date vesion of the afnmr functionality, and is the one that will be maintained going forward.)

The basic ideas are presented in the following papers:

  1. K. Osapay and D.A. Case. A new analysis of proton chemical shifts in proteins. J. Am. Chem. Soc. 113, 9436-9444 (1991).

  2. K. Osapay and D.A. Case. Analysis of proton chemical shifts in regular secondary structure of proteins. J. Biomol. NMR 4, 215-230 (1994).

  3. D.F. Sitkoff and D.A. Case. Density functional calculations of proton chemical shifts in model peptide systems. J. Am. Chem. Soc. 119, 12262-12273 (1997).

  4. D. Sitkoff and D.A. Case. Theories of chemical shift anisotropies in proteins and nucleic acids. Prog. NMR Spectr. 32, 165-190 (1998).

  5. A. Dejaegere and D.A. Case. Density functional study of ribose and deoxyribose chemical shifts. J. Phys. Chem. 102, 5280-5289 (1998).

  6. A.P. Dejaegere, R.A. Bryce and D.A. Case. An empirical analysis of proton chemical shifts in nucleic acids. In Modeling NMR Chemical Shifts, J.C. Facelli and A.C. de Dios, eds. (Washington, American Chemical Society, 1999), pp. 194-206.

  7. X.P Xu and D.A. Case. Automated prediction of 15N, 13Cα, 13Cβ and 13C' chemical shifts in proteins using a density functional database. J. Biomol. NMR. 21, 321-333 (2001).

  8. X.P. Xu and D.A. Case. Probing multiple effects on 15N, 13Cα, 13Cβ and 13C' chemical shifts in peptides using density functional theory. Biopolymers 65, 408-423 (2002).

  9. S. Moon and D.A. Case. A new model for chemical shifts of amide hydrogens in proteins. J. Biomol. NMR 38, 139-150 (2007).

  10. X. He, B. Wang, and K.M. Merz, Jr. Protein NMR Chemical Shift Calculations Based on the Automated Fragmentation QM/MM Approach. J. Phys. Chem. B 113, 10380-10388 (2009).

  11. T. Zhu, X. He, and J.Z.H. Zhang. Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Phys. Chem. Chem. Phys. 14, 7837-7845 (2012)

  12. T. Zhu, J.Z.H. Zhang, and X. He. Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model. J. Chem. Theory Comput. 9, 2104-2114 (2013)

  13. S. Tang and D.A. Case. Calculation of chemical shift anisotropy in proteins. J. Biomol. NMR 51, 303-312 (2011).

  14. D.A. Case. Chemical shifts in biomolecules. Curr. Opin. Struct. Biol. 23, 172-176 (2013).

  15. J. Swails, T. Zhu, X. He and David A. Case. AFNMR: Automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J. Biomol. NMR 63, 125-139 (2015).

Here are some recent applications:

The latest version (5.5, June, 2018) can be obtained from:

shifts-5.5.tar.gz

Some version history:

You will need the AmberTools package (see http://ambermd.org/AmberTools.php, in order to compile SHIFTS. Both AmberTools and SHIFTS are distributed under the GNU General Public License (GPL).

The latest version (1.0, October, 2018) of the afnmr package can be obtained from:

afnmr-1.0.tar.bz2

Installation and usage instructions are in the afnmr.pdf file, in the "doc" folder.



Updated on February 18, 2019. Comments to case@biomaps.rutgers.edu