• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of pnasPNASInfo for AuthorsSubscriptionsAboutThis Article
Proc Natl Acad Sci U S A. Jun 1, 1992; 89(11): 4918–4922.
PMCID: PMC49199

Optimal protein-folding codes from spin-glass theory.

Abstract

Protein-folding codes embodied in sequence-dependent energy functions can be optimized using spin-glass theory. Optimal folding codes for associative-memory Hamiltonians based on aligned sequences are deduced. A screening method based on these codes correctly recognizes protein structures in the "twilight zone" of sequence identity in the overwhelming majority of cases. Simulated annealing for the optimally encoded Hamiltonian generally leads to qualitatively correct structures.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.3M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Friedrichs MS, Wolynes PG. Toward protein tertiary structure recognition by means of associative memory hamiltonians. Science. 1989 Oct 20;246(4928):371–373. [PubMed]
  • Hopfield JJ. Neural networks and physical systems with emergent collective computational abilities. Proc Natl Acad Sci U S A. 1982 Apr;79(8):2554–2558. [PMC free article] [PubMed]
  • Bryngelson JD, Wolynes PG. Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7524–7528. [PMC free article] [PubMed]
  • Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 1991;9(1):56–68. [PubMed]
  • Doolittle RF. Searching through sequence databases. Methods Enzymol. 1990;183:99–110. [PubMed]
  • Bowie JU, Lüthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991 Jul 12;253(5016):164–170. [PubMed]
  • Lüthy R, McLachlan AD, Eisenberg D. Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins. 1991;10(3):229–239. [PubMed]
  • Finkelstein AV, Reva BA. A search for the most stable folds of protein chains. Nature. 1991 Jun 6;351(6326):497–499. [PubMed]
  • Friedrichs MS, Goldstein RA, Wolynes PG. Generalized protein tertiary structure recognition using associative memory Hamiltonians. J Mol Biol. 1991 Dec 20;222(4):1013–1034. [PubMed]
  • Sasai M, Wolynes PG. Molecular theory of associative memory Hamiltonian models of protein folding. Phys Rev Lett. 1990 Nov 19;65(21):2740–2743. [PubMed]
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. [PubMed]
  • Devereux J, Haeberli P, Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. [PMC free article] [PubMed]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Cited in Books
    Cited in Books
    PubMed Central articles cited in books
  • Compound
    Compound
    PubChem Compound links
  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...