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.

Note: The SHIFTS package used to include quantum calculations of shifts. These have been separated into a separate package, afnmr.

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).

How to obtain SHIFTS

The latest version (5.6, November, 2023) is now a part of the "nabc" repository:

github.com/dacase/nabc.

There is no longer a dependency on AmberTools.

Some version history:



Updated on October 3, 2024. Comments to david.case@rutgers.edu