Literature DB >> 1409599

Protein tertiary structure recognition using optimized Hamiltonians with local interactions.

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

Abstract

Protein folding codes embodying local interactions including surface and secondary structure propensities and residue-residue contacts are optimized for a set of training proteins by using spin-glass theory. A screening method based on these codes correctly matches the structure of a set of test proteins with proteins of similar topology with 100% accuracy, even with limited sequence similarity between the test proteins and the structural homologs and the absence of any structurally similar proteins in the training set.

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Year:  1992        PMID： 1409599      PMCID： PMC50058          DOI： 10.1073/pnas.89.19.9029

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


  22 in total

1.  Assessment of protein models with three-dimensional profiles.

Authors:  R Lüthy; J U Bowie; D Eisenberg
Journal:  Nature       Date:  1992-03-05       Impact factor: 49.962

2.  Prediction of protein folding from amino acid sequence over discrete conformation spaces.

Authors:  G M Crippen
Journal:  Biochemistry       Date:  1991-04-30       Impact factor: 3.162

3.  A lattice model for protein structure prediction at low resolution.

Authors:  D A Hinds; M Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  1992-04-01       Impact factor: 11.205

4.  Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

Authors:  M J Sippl; S Weitckus
Journal:  Proteins       Date:  1992-07

5.  Generalized protein tertiary structure recognition using associative memory Hamiltonians.

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

6.  Toward protein tertiary structure recognition by means of associative memory hamiltonians.

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

7.  Simulations of the folding of a globular protein.

Authors:  J Skolnick; A Kolinski
Journal:  Science       Date:  1990-11-23       Impact factor: 47.728

8.  Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors:  W Kabsch; C Sander
Journal:  Biopolymers       Date:  1983-12       Impact factor: 2.505

Review 9.  The anatomy and taxonomy of protein structure.

Authors:  J S Richardson
Journal:  Adv Protein Chem       Date:  1981

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
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  61 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.  A method for parameter optimization in computational biology.

Authors:  J B Rosen; A T Phillips; S Y Oh; K A Dill
Journal:  Biophys J       Date:  2000-12       Impact factor: 4.033

5.  Protein threading by learning.

Authors:  I Chang; M Cieplak; R I Dima; A Maritan; J R Banavar
Journal:  Proc Natl Acad Sci U S A       Date:  2001-11-20       Impact factor: 11.205

6.  Improved recognition of native-like protein structures using a family of designed sequences.

Authors:  Patrice Koehl; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2002-01-08       Impact factor: 11.205

7.  Radially softening diffusive motions in a globular protein.

Authors:  S Dellerue; A J Petrescu; J C Smith; M C Bellissent-Funel
Journal:  Biophys J       Date:  2001-09       Impact factor: 4.033

8.  Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease.

Authors:  Nese Kurt; Turkan Haliloglu; Celia A Schiffer
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

9.  Design of an optimal Chebyshev-expanded discrimination function for globular proteins.

Authors:  Boris Fain; Yu Xia; Michael Levitt
Journal:  Protein Sci       Date:  2002-08       Impact factor: 6.725

10.  Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices.

Authors:  Andrew E Torda; James B Procter; Thomas Huber
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971
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