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, C`alpha`, C`beta` and C' shifts in proteins, using a database based on DFT calculations on peptides. The basic ideas are presented in the following papers:

  • K. Osapay and D.A. Case. A new analysis of proton chemical shifts in proteins. Journal of the Americal Chemical Society 113, 9436-9444 (1991).

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

  • 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).

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

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

  • 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.

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

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

  • S. Moon and D.A. Case. A new model for chemical shifts of amide hydrogens in proteins. (Submitted for publication).

    The latest version (4.3, May, 2009) can be obtained from:

    shifts-4.3.tar.gz

    Version 4.1.2 is a minor bug-fix release compared to versions 4.1 and 4.1.1, required primarily for some Linux machines and for compatibility with the latest version of NAB. If you have version 4.1 or 4.1.1, and it passes the test suite, you should not need to download the updated version.

    Version 4.2 adds a new model for estimating amide proton shifts in proteins. It will be described in the last paper listed above; if you can't wait, please contact the authors for more information.

    Version 4.3 just has a minor fix to the lsq program, and updates the documentation.

    You will need the NAB program (see the menu item at the left) in order to compile SHIFTS. Both NAB and SHIFTS are distributed under the GNU General Public License (GPL).

    A Web service that will return shift predictions based on a pdb file provided by a remote user can be found at:

    http://casegroup.rutgers.edu/qshifts/qshifts.htm


    Updated on November 17, 2009. Comments to case@biomaps.rutgers.edu