Chemical Shift Analysis

Talos+ uses a database of chemical shifts of proteins for which high resolution crystal structures are available. By matching amino acid type and chemical shifts (N, HN, Cα, Cβ, CO) to triplets of amino acids from the database, it predicts the average φ and ψ angles for your protein. Also available via the WeNMR Webportal.

This program is similar to TALOS but uses a Bayesian inferential method to predict backbone dihedral angles from chemical shifts. It is automatically included in the CCPNmr Analysis package or can be downloaded from Sourceforge and instructions are available via the Analysis manual.

Like TALOS+ and DANGLE, this program uses 1H, 13C and 15N chemical shifts and sequence homology to predict torsion angles. It runs as a webserver and can predict χ1 and ω angles as well as the more conventional φ and ψ angles.

The SHIFTX2 server predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input.

Sparta+ will predict backbone chemical shifts from a 3D protein structure.

The ProShift server predicts 1H, 13C and 15N chemical shifts based on a 3D input structure.

The CamShift server predicts backbone chemical shifts from a 3D structure.

The SHIFTS server predicts backbone chemical shifts from a 3D structure. It uses a database of density functional theory (DFT) calculations on over 2000 peptides.

The CheShift server predicts Cα chemical shifts from a 3D structure based on a quantum mechanics database.

SHIFTCOR compares, identifies, corrects and re-referencs 1H, 13C and 15N backbone chemical shifts of peptides and proteins by comparing the observed chemical shifts with the predicted chemical shifts derived from the 3D structure (PDB corrdinates) of the protein(s) of interest.

The Re-referenced Protein Chemical Shift Database (RefDB) is a database of carefully corrected or re-referenced chemical shifts, derived from the BioMagRes Bank (BMRB). The process involves predicting protein 1H, 13C and 15N chemical shifts using X-ray or NMR coordinate data via SHIFTX and then comparing those predictions to the observed shifts reported in the BMRB (via SHIFTCOR). RefDB provides a standard chemical shift resource for NMR spectroscopists, wishing to derive or compute chemical shift trends in peptides and proteins.

SHIFTX2, SHIFTCOR and RefDB all come from David Wishart’s group. His lab has done a lot of work on chemical shifts of proteins over the years and they have several more web servers which will do varying things including predicting chemical shifts from the structure or sequence of a protein, predicting secondary structure from chemical shifts, or automatic assignment and structure calculation using an HNCACB peak list as input.