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

pulldown Chain: Choose the molecular system chain to make predictions for

pulldown Shift List: Select the shift list to take input chemical shifts from

pulldown Type: Select the algorithm script for this chain

pulldown 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

button Run CamCoil Prediction!: Run the CamCoil method to predict chemical shifts from sequence

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