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.

References and further Reading
  1. Theory of protein folding: the energy landscape perspective
    Onuchic JN, Luthey-Schulten Z, Wolynes PG
    Annu Rev Phys Chem - 1997 - [pdf]

  2. Spin glasses and the statistical mechanics of protein folding
    Bryngelson JD, Wolynes PG
    Proc Natl Acad Sci USA - 1987 - [pdf]

  3. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
    Clementi C, Nymeyer H, Onuchic JN
    J Mol Biol - 2000 - [pdf]

  4. Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model
    Koga N, Takada S
    J Mol Biol - 2001 - [pdf]

  5. Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates
    Chavez LL, Onuchic JN, Clementi C
    J Am Chem Soc - 2004 - [pdf]

  6. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family
    Ferreiro DU, Cho SS, Komives EA, Wolynes PG
    J Mol Biol - 2005 - [pdf]

  7. Protein topology determines binding mechanism
    Levy Y, Wolynes PG, Onuchic JN
    Proc Natl Acad Sci USA - 2004 - [pdf]

  8. Domain swapping is a consequence of minimal frustration
    Yang S, Cho SS, Levy Y, Cheung MS, Levine H, Wolynes PG, Onuchic JN
    Proc Natl Acad Sci USA - 2004 - [pdf]

  9. The Energy Lanscapes and Motions of Poteins
    Frauenfelder H, Sligar SG, Wolynes PG
    Science - 1991 - [pdf]

  10. The spectrum of biomolecular states and motions
    Hegler JA, Weinkam P , Wolynes PG
    HFSP Journal - 2008 - [pdf]

  11. Localizing frustration in native proteins and protein assemblies
    Ferreiro DU, Hegler JA, Komives EA, Wolynes PG
    Proc Natl Acad Sci USA - 2007 - [pdf]

  12. Supplementary Methods to reference 11 [pdf]

  13. Water in protein structure prediction
    Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG
    Proc Natl Acad Sci USA - 2003 - [pdf]

  14. Consequences of localized frustration for the folding mechanism of the IM7 protein
    Sutto L, Latzer J, Hegler JA, Ferreiro DU, Wolynes PG
    Proc Natl Acad Sci USA - 2007 - [pdf]

  15. The capillarity picture and the kinetics of one-dimensional protein folding
    Ferreiro DU, Wolynes PG
    Proc Natl Acad Sci USA - 2008 - [pdf]

  16. On the role of frustration in the energy landscapes of allosteric proteins
    Ferreiro DU, Hegler JA, Komives EA, Wolynes PG
    Proc Natl Acad Sci USA - 2011 - [pdf]


How to cite this application

Protein frustratometer: a tool to localize energetic frustration in protein molecules.
Michael Jenik; R. Gonzalo Parra; Leandro G. Radusky; Adrian Turjanski; Peter G. Wolynes; Diego U. Ferreiro.
Nucleic Acids Research 2012; doi: 10.1093/nar/gks447
[Abstract] [Full Text] [pdf]

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