Data Analysis : Predict Shifts from Sequence
Predict Protein Shifts from Sequence
This popup window is designed to allow the prediction of chemical shifts
for a protein chain from the sequence (so with no structural information),
using the (external) program CamCoil.
The Options to select are the Chain for which the prediction is made, and
the prediction type and the pH used for the prediction, and also the Shift
List, which is not used for the prediction but is used for the comparison
with the prediction.
CamCoil has two variations, one for the prediction of random coil chemical
shifts and one for prediction of protein loops chemical shifts.
The Chemical Shift Predictions table lists the atoms in the chain.
For each atom the data listed is the residue number, residue type, atom
name, first shift found for that atom in the chosen shiftList, chemical
shift predicted by CamCoil, and the difference between the actual shift
and the predicted shift (if both exist).
To run the prediction click on the “Run CamCoil Prediction!” button. This
does not store any predicted shifts in the project.
Caveats & Tips
References
The CamCoil programme:
http://www-vendruscolo.ch.cam.ac.uk/camcoil.php
*A. De Simone, A. Cavalli, S-T. D. Hsu, W. Vranken and M. Vendruscolo
Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins.
J. Am. Chem. Soc. 131(45):16332-3
Main Panel
Options
Chain: Choose the molecular system chain to make predictions for
Shift List: Select the shift list to take input chemical shifts from
Type: Select the algorithm script for this chain
pH: Select the pH to make the prediction for
Chemical Shift Predictions
Table 1 |
Res Num |
Residue number in chain |
Res Type |
Residue type code |
Atom Name |
Atom name |
Actual Shift |
Actual shift (first one it finds for atom in chosen shiftList) |
Predicted Shift |
CamCoil predicted shift |
Difference |
Predicted - Actual |
Run CamCoil Prediction!: Run the CamCoil method to predict chemical shifts from sequence