What is DynaMine
DynaMine is a fast predictor of protein backbone dynamics using only sequence information as input. Given a protein sequence, DynaMine predicts backbone flexibility at the residue-level in the form of backbone N-H S2 order parameter values. These S2 values represent how restricted the movement of the atomic bond vector is with respect to the molecular reference frame. A value of 1 means complete order (stable conformation), while a value of 0 means fully random bond vector movement (highly dynamic). Read more in DynaMine in a nushell.
A detailed description of the underlying predictor and its performance also with respect to disorder can be found here.
How to use DynaMine
Using DynaMine is very simple. You just need to:
- go to the submission page
- copy-paste in the text area a sequence in FASTA format or upload a file containing it or insert directly a Uniprot identifier.
- click to send the job to the DynaMine server
- wait just a few seconds for the results! The results will appear in the same web-browser window.
You can ask for an example of sequence in FASTA format or of Uniprot identifier by clicking on or clearing all the settings by clicking on .
Once you click the button you will see a page like the one displayed below (Figure 2):
This page is automatically refreshed every 10 seconds and reports the status of your job (queued, running or finished).
When the results are available, they are displayed on this same page.
You can also bookmark it to check the results later.
DynaMine predictions are displayed in different formats (see the example page in Figure 3):
- An annotated plot of the predictions (y axis) along the amino acid sequence (x axis) showing the backbone dynamics profile of your sequence. More rigid and flexible regions are separated by the grey band.
- A graphical representation of your sequence where the size of the residues reflects how likely they are to be “ordered”. The same holds for the colour temperature ranging from red (flexible – low predicted S2 value) to blue (ordered – high predicted S2 value).
- Detailed predictions reported for the residues with S2 order parameter greater than 0.9 as predicted by DynaMine. Two pop-up menus provide you with the possibility of filtering the predictions by value greater or smaller than a given threshold.
- A link for downloading the complete list of DynaMine predictions for the sequence of interest.
Additionally all the graphical depictions of the results can be downloaded as pictures in high resolution.
A link to a zip file containing all DynaMine results (predictions and graphical depictions) is provided on top of this page.