Literature DB >> 8197177

An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure.

A Monge1, R A Friesner, B Honig.   

Abstract

An algorithm is described to assemble the three-dimensional fold of a protein starting from its secondary structure. A reduced representation of the polypeptide chain is used together with a crude potential based on pair hydrophobicities. The method is shown to be successful in locating the native topology for two 4-alpha-helix bundles, myohemerythrin and cytochrome b-562.

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Year:  1994        PMID： 8197177      PMCID： PMC43923          DOI： 10.1073/pnas.91.11.5027

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


  19 in total

Review 1.  Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds.

Authors:  G Casari; M J Sippl
Journal:  J Mol Biol       Date:  1992-04-05       Impact factor: 5.469

2.  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

3.  Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions.

Authors:  M J Rooman; J P Kocher; S J Wodak
Journal:  J Mol Biol       Date:  1991-10-05       Impact factor: 5.469

4.  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

5.  Energetic approach to the folding of four alpha-helices connected sequentially.

Authors:  L Carlacci; K C Chou
Journal:  Protein Eng       Date:  1990-05

6.  Simulations of the folding of a globular protein.

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

7.  Energetics of the structure of the four-alpha-helix bundle in proteins.

Authors:  K C Chou; G M Maggiora; G Némethy; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  1988-06       Impact factor: 11.205

8.  Diffusion-collision model for the folding kinetics of myoglobin.

Authors:  D Bashford; F E Cohen; M Karplus; I D Kuntz; D L Weaver
Journal:  Proteins       Date:  1988

9.  On the prediction of protein structure: The significance of the root-mean-square deviation.

Authors:  F E Cohen; M J Sternberg
Journal:  J Mol Biol       Date:  1980-04       Impact factor: 5.469

10.  Origins of structure in globular proteins.

Authors:  H S Chan; K A Dill
Journal:  Proc Natl Acad Sci U S A       Date:  1990-08       Impact factor: 11.205
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  9 in total

1.  Predicting the structures of 18 peptides using Geocore.

Authors:  K Ishikawa; K Yue; K A Dill
Journal:  Protein Sci       Date:  1999-04       Impact factor: 6.725

2.  Designability of alpha-helical proteins.

Authors:  Eldon G Emberly; Ned S Wingreen; Chao Tang
Journal:  Proc Natl Acad Sci U S A       Date:  2002-08-12       Impact factor: 11.205

3.  Toward predicting protein topology: an approach to identifying beta hairpins.

Authors:  Xavier de la Cruz; E Gail Hutchinson; Adrian Shepherd; Janet M Thornton
Journal:  Proc Natl Acad Sci U S A       Date:  2002-08-12       Impact factor: 11.205

4.  An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data.

Authors:  Sarel J Fleishman; Susan Harrington; Richard A Friesner; Barry Honig; Nir Ben-Tal
Journal:  Biophys J       Date:  2004-08-31       Impact factor: 4.033

5.  The importance of larger data sets for protein secondary structure prediction with neural networks.

Authors:  J M Chandonia; M Karplus
Journal:  Protein Sci       Date:  1996-04       Impact factor: 6.725

6.  Folding proteins with a simple energy function and extensive conformational searching.

Authors:  K Yue; K A Dill
Journal:  Protein Sci       Date:  1996-02       Impact factor: 6.725

7.  Proposed structure of putative glucose channel in GLUT1 facilitative glucose transporter.

Authors:  H Zeng; R Parthasarathy; A L Rampal; C Y Jung
Journal:  Biophys J       Date:  1996-01       Impact factor: 4.033

8.  A fast conformational search strategy for finding low energy structures of model proteins.

Authors:  T C Beutler; K A Dill
Journal:  Protein Sci       Date:  1996-10       Impact factor: 6.725

9.  Relationship between protein structure and geometrical constraints.

Authors:  O Lund; J Hansen; S Brunak; J Bohr
Journal:  Protein Sci       Date:  1996-11       Impact factor: 6.725
  9 in total

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