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Literature DB >> 1594594

Optimal protein-folding codes from spin-glass theory.

R A Goldstein¹, Z A Luthey-Schulten, P G Wolynes.

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.

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Year: 1992 PMID： 1594594 PMCID： PMC49199 DOI： 10.1073/pnas.89.11.4918

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

12 in total

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Authors: C Sander; R Schneider
Journal: Proteins Date: 1991

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Authors: M S Friedrichs; R A Goldstein; P G Wolynes
Journal: J Mol Biol Date: 1991-12-20 Impact factor: 5.469

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Authors: J U Bowie; R Lüthy; D Eisenberg
Journal: Science Date: 1991-07-12 Impact factor: 47.728

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Authors: M S Friedrichs; P G Wolynes
Journal: Science Date: 1989-10-20 Impact factor: 47.728

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Authors: R Lüthy; A D McLachlan; D Eisenberg
Journal: Proteins Date: 1991

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Authors: F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal: J Mol Biol Date: 1977-05-25 Impact factor: 5.469

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Authors: R F Doolittle
Journal: Methods Enzymol Date: 1990 Impact factor: 1.600

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Authors: J Devereux; P Haeberli; O Smithies
Journal: Nucleic Acids Res Date: 1984-01-11 Impact factor: 16.971

9. Neural networks and physical systems with emergent collective computational abilities.

Authors: J J Hopfield
Journal: Proc Natl Acad Sci U S A Date: 1982-04 Impact factor: 11.205

10. Spin glasses and the statistical mechanics of protein folding.

Authors: J D Bryngelson; P G Wolynes
Journal: Proc Natl Acad Sci U S A Date: 1987-11 Impact factor: 11.205

86 in total

1. A statistical mechanical method to optimize energy functions for protein folding.

Authors: U Bastolla; M Vendruscolo; E W Knapp
Journal: Proc Natl Acad Sci U S A Date: 2000-04-11 Impact factor: 11.205

2. Scoring functions in protein folding and design.

Authors: R I Dima; J R Banavar; A Maritan
Journal: Protein Sci Date: 2000-04 Impact factor: 6.725

3. Analysis of knowledge-based protein-ligand potentials using a self-consistent method.

Authors: J Shimada; A V Ishchenko; E I Shakhnovich
Journal: Protein Sci Date: 2000-04 Impact factor: 6.725

4. Investigation of routes and funnels in protein folding by free energy functional methods.

Authors: S S Plotkin; J N Onuchic
Journal: Proc Natl Acad Sci U S A Date: 2000-06-06 Impact factor: 11.205

5. Folding protein models with a simple hydrophobic energy function: the fundamental importance of monomer inside/outside segregation.

Authors: A F Pereira De Araújo
Journal: Proc Natl Acad Sci U S A Date: 1999-10-26 Impact factor: 11.205