nmrserver_logo From the Bax Group at the National Institutes of Health ...
PROMEGA Server:
Prediction of Proline cis/trans Conformation from Chemical Shifts and Sequence

promegaLogo As described in the paper:
Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts.
Yang Shen and Ad Bax J. Biomol. NMR, 46, 199-204 (2009).

PROMEGA Software Web Site:
http://spin.niddk.nih.gov/bax/software/PROMEGA

Contacts:
Yang Shen     shenYang@niddk.nih.gov
Ad Bax     bax@nih.gov

Chemical Shift Input
The input table of chemical shifts and sequence information. The format of the table is described in the PROMEGA Web Page. Example: plastocyanin.tab (PRO residues 16 and 36 in cis conformation).
As an alternative, the input table of chemical shifts and sequence information can be specified as a BMRB NMR-Star format file. In order to use NMR-Star format as input to PROMEGA, the BMRB file should have chemical shift information and complete sequence information for a single protein only. When input is supplied as a BMRB file, CYS residues with a CB shift of 34ppm or less are assumed to be reduced, and HIS residues in tables with a listed pH of 6.0 or less are assumed to be protonated. Example: bmr7234.str (PRO residue 146 in cis conformation).
Prediction Options
Apply Offset Correction Select this option to test the input chemical shift referencing and apply an automated offset correction if needed.
Apply Deuterium Correction Select this option if the input CA and CB chemical shifts need to be adjusted for deuterium isotope effect. Leave this option off if you have already adjusted the CA and CB shifts.
Optional input PDB file for comparison. If a PDB file is given, PROMEGA prediction results will also include the corresponding residue types and omega angles from the PDB structure. It is assumed that the sequence of the PDB file matches the sequence of the input chemical shift table. Examples: plastocyanin.pdb and 7234.pdb
Submission Details
Email:
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last update: May 23 2012