PROMEGA

PROMEGA


Synopsis

Proline Omega angle prediction from sequence and chemical shifts.

Description

Promega is a system for empirical prediction of Xaa-Pro peptide bond conformation from backbone NMR chemical shifts (N, HN, HA, CA, CB, CO) and amino acid type information of the residues neighboring Pro. Using a database of proteins of known structure, the NMR chemical shift pattern and the PDB-extracted amino acid preference of the cis and trans Xaa-Pro dipeptide bond conformations are used to calculate a cis/trans probability score from the backbone and CB chemical shifts of the proline and its neighboring residues. Promega typically offers unique identification for Xaa-Pro peptide bonds in cases where Pro-CG chemical shifts are available, but even with CG shifts lacking it often provides a strong indication for the cis or trans state of the bond, making it applicable to studies of larger proteins where obtaining CG assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and 13C chemical shifts.

URL

https://spin.niddk.nih.gov/bax/software/PROMEGA/

Versions

NMRbox Version Software Version
1.0.0 1.40F1_rev2012.029.12.03,
2.0.0 1.40F1_rev2012.029.12.03,
3.0.0 1.40F1_rev2012.029.12.03,

Keywords

  • Torsion Angle Prediction

Citations

Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts
Shen Yang, Bax Ad,
Journal of biomolecular NMR. 2010; 46(3): 199--204