Frequently Asked Questions
What are those lines joining the Calphas over my structure?
They are a cartoon of the interactions between pairs of aminoacids:
'minimally frustrated' interactions are favorable for folding the
provided sequence in the provided structure.
Highly frustrated interactions are in conflict with folding the
provided sequence and structure. They reflect that other evolutionary
pressures (besides folding) might be at play selecting them. They are
usually found enriched in proteins functional sites (visit our
study cases page).
What are those graphs below the structure?
The first one is a 'contact map', each dot represents
pair-interactions between aminoacids, numbered on the axis. They are
colored according to their frustration index.
The other ones are projections of the contact information on the sequence space.
What are the 'neutral' contacts?
'Neutral' interactions are not particularly favorable nor
unfavorable for folding. They might reflect intrinsic evolutionary
drift. For clarity, the neutral contacts are not draw on the structure
Can I download the results?
Yes you can. Fetch the results page of your job by entering your job ID in the field below, or by following the link contained in the email we sent you. Then click in the Download link in the bottom of the results page.
Hey! You changed the numbering of my pdb file ! ?
We might have, sorry. In the present release the pdb files are
renumbered starting from 1, gaps are ignored, and only the most common
20 aminoacids are taken into account.
What about secondary structure propensity ?
At present the server does not take into account any secondary
structure energy. Only the tertiary contact energies are evaluated
according to the AMW energy function .
What about side-chain rotamers ?
No energetic terms for side-chains are explicitly taken into
account. Only Calpha and Cbeta positions and energies are evaluated in
the AMW energy function.
I do not see any plots on the results page.
This is most likely an error due to oversize. We are currently
limiting the runs to 1000 residues. In case you need to run a bigger
system, please contact us.
May I use the frustratometer results ?
We'll be glad if they are useful. Please cite us in case you do.