Bax Group TALOS-N Server

From the Bax Group at the National Institutes of Health ...
TALOS-N Server:
Prediction of Protein Backbone and Sidechain Torsion Angles from Chemical Shifts

As described in the paper:
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
Yang Shen, and Ad Bax. J. Biomol. NMR 56, 227-241(2013). (doi)

TALOS-N Software Web Site:
http://spin.niddk.nih.gov/bax/software/TALOS-N
Java Viewer (jRAMA) for displaying TALOS-N results:
http://spin.niddk.nih.gov/bax/software/TALOS-N/JRAMA

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

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Chemical Shift Input

The input table of chemical shifts and sequence information. The format of the table is described in the TALOS Web Page. Example: ubiq.tab
As an alternative, the input table of chemical shifts and sequence information can be specified as a BMRB NMR-Star format (v2.1 or v3.1) file. In order to use NMR-Star format as input to TALOS-N, 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: ubiq.str
(Click here to see a complete list and description of all allowed formats.)

Prediction Options

Exclude Identical Sequences

Select this option to exclude database proteins which have an amino acid sequence identical to the one given in the input chemical shift table.

Apply Offset Correction

Select this option to test the input chemical shift referencing and apply an automated offset correction if needed.

	Include 1H Shifts (Default Mode)
	Ignore 1H Shifts (No-Proton Mode)
	Auto 1H Mode

In Default Mode, TALOS-N will use 1H, 13C and 15N shifts to make a prediction. If the Ignore 1H Shifts option is selected, TALOS-N will use 13C/15N shifts only, and ignore any 1H shifts; this is called No-Proton Mode. The No-Proton Mode is useful if no 1H shifts are available (e.g. for solids) or if the 1H shifts contain many outliers (e.g. paramagnetic proteins). The No-Proton Mode may also be useful if only HA shifts are missing, as with deuterated proteins. If the Auto 1H Mode is selected, TALOS-N will use the No-Proton mode automatically if the input contains no 1H shifts of any kind. Example Shift Input: ubiqss.str, BMRB-Format Solid State Chemical Shifts.

Apply Deuterium Correction

Deuterium Correction (Deuterated Proteins Only) (optional). 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, TALOS-N classification results will be marked as BAD at every residue where the TALOS-N prediction differs substantially from the angles found in the given PDB structure. The sequence of the PDB file must match the sequence of the input chemical shift table. Example: ubiq.pdb

Submission Details

Email:

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last update: April 30, 2013