Frustratometer


There is a new version for this service, check it here. The Frustratometer is an Energy Landscape Theory inspired algorithm that aims at quantifying the degree of local frustration manifested in protein molecules. Frustration is a useful concept for gaining insight to the proteins biological behavior by analyzing how the energy is distributed in protein structures and how mutations or conformational changes shift the energy distributions. Sites of high local frustration often indicate biologically important regions such as binding or allosteric sites. Minimally frustrated linkages constitute a stable folding core of the molecule.

FAQs
  • 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 by default.


  • 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 [12].


  • 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.

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