References and Further Reading
- Theory of protein folding: the energy landscape perspective
Onuchic JN, Luthey-Schulten Z, Wolynes PG
Annu Rev Phys Chem - 1997 - [pdf] - Spin glasses and the statistical mechanics of protein folding
Bryngelson JD, Wolynes PG
Proc Natl Acad Sci USA - 1987 - [pdf] - 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] - 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] - 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] - 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] - Protein topology determines binding mechanism
Levy Y, Wolynes PG, Onuchic JN
Proc Natl Acad Sci USA - 2004 - [pdf] - 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] - The Energy Lanscapes and Motions of Poteins
Frauenfelder H, Sligar SG, Wolynes PG
Science - 1991 - [pdf] - The spectrum of biomolecular states and motions
Hegler JA, Weinkam P , Wolynes PG
HFSP Journal - 2008 - [pdf] - Localizing frustration in native proteins and protein assemblies
Ferreiro DU, Hegler JA, Komives EA, Wolynes PG
Proc Natl Acad Sci USA - 2007 - [pdf] - Supplementary Methods to reference 11 [pdf]
- Water in protein structure prediction
Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG
Proc Natl Acad Sci USA - 2003 - [pdf] - 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] - The capillarity picture and the kinetics of one-dimensional protein folding
Ferreiro DU, Wolynes PG
Proc Natl Acad Sci USA - 2008 - [pdf] - 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]
This application has been useful for (and been cited by):
The energy landscape analysis of cancer mutations in protein kinases.
Dixit A, Verkhivker GM.
PLoS One. (2011) 6(10):e26071
Pubmed
A potential in silico antibody-antigen based diagnostic test for precise identification of Acinetobacter baumannii.
Rahbar MR, et al.
(2011) J Theor Biol. 294C:29-39
Pubmed
A survey of lambda repressor fragments from two-state to downhill folding.
Liu F, Gao YG, Gruebele M.
(2010) J Mol Biol. 397(3):789-98
Pubmed
The capillarity picture and the kinetics of one-dimensional protein folding.
Ferreiro DU, Wolynes PG.
(2008) Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):9853-4.
Pubmed
Consequences of localized frustration for the folding mechanism of the IM7 protein.
Sutto L, Lätzer J, Hegler JA, Ferreiro DU, Wolynes PG.
(2007) Proc Natl Acad Sci U S A. Dec 11;104(50):19825-30
Pubmed