Literature DB >> 7667278

Predicting coiled coils by use of pairwise residue correlations.

B Berger1, D B Wilson, E Wolf, T Tonchev, M Milla, P S Kim.   

Abstract

A method is presented that predicts coiled-coil domains in protein sequences by using pairwise residue correlations obtained from a (two-stranded) coiled-coil database of 58,217 amino acid residues. A program called PAIRCOIL implements this method and is significantly better than existing methods at distinguishing coiled coils from alpha-helices that are not coiled coils. The database of pairwise residue correlations suggests structural features that stabilize or destabilize coiled coils.

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Year:  1995        PMID： 7667278      PMCID： PMC41136          DOI： 10.1073/pnas.92.18.8259

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


  34 in total

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Journal:  Macromolecules       Date:  1975 Jul-Aug       Impact factor: 5.985

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Journal:  Biochem J       Date:  1986-06-15       Impact factor: 3.857

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Journal:  Annu Rev Biophys Biophys Chem       Date:  1987

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Authors:  R C Lu; A Wong
Journal:  J Biol Chem       Date:  1985-03-25       Impact factor: 5.157

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Authors:  A D McLachlan; J Karn
Journal:  J Mol Biol       Date:  1983-03-15       Impact factor: 5.469

6.  Periodic charge distributions in the myosin rod amino acid sequence match cross-bridge spacings in muscle.

Authors:  A D McLachlan; J Karn
Journal:  Nature       Date:  1982-09-16       Impact factor: 49.962

7.  Coiled-coils in alpha-helix-containing proteins: analysis of the residue types within the heptad repeat and the use of these data in the prediction of coiled-coils in other proteins.

Authors:  D A Parry
Journal:  Biosci Rep       Date:  1982-12       Impact factor: 3.840

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Authors:  D Stone; L B Smillie
Journal:  J Biol Chem       Date:  1978-02-25       Impact factor: 5.157

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Authors:  S Y Lau; C Sanders; L B Smillie
Journal:  J Biol Chem       Date:  1985-06-25       Impact factor: 5.157

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Authors:  S Y Lau; A K Taneja; R S Hodges
Journal:  J Biol Chem       Date:  1984-11-10       Impact factor: 5.157
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  222 in total

1.  Identification and characterization of a negative regulator of FtsZ ring formation in Bacillus subtilis.

Authors:  P A Levin; I G Kurtser; A D Grossman
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-17       Impact factor: 11.205

2.  The role of position a in determining the stability and oligomerization state of alpha-helical coiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins.

Authors:  K Wagschal; B Tripet; P Lavigne; C Mant; R S Hodges
Journal:  Protein Sci       Date:  1999-11       Impact factor: 6.725

3.  An engineered leucine zipper a position mutant with an unusual three-state unfolding pathway.

Authors:  H Zhu; S A Celinski; J M Scholtz; J C Hu
Journal:  Protein Sci       Date:  2001-01       Impact factor: 6.725

4.  Functional domains present in the mycobacterial hemagglutinin, HBHA.

Authors:  G Delogu; M J Brennan
Journal:  J Bacteriol       Date:  1999-12       Impact factor: 3.490

5.  An ancestral MADS-box gene duplication occurred before the divergence of plants and animals.

Authors:  E R Alvarez-Buylla; S Pelaz; S J Liljegren; S E Gold; C Burgeff; G S Ditta; L Ribas de Pouplana; L Martínez-Castilla; M F Yanofsky
Journal:  Proc Natl Acad Sci U S A       Date:  2000-05-09       Impact factor: 11.205

6.  Coiled-coil domain-mediated FRQ-FRQ interaction is essential for its circadian clock function in Neurospora.

Authors:  P Cheng; Y Yang; C Heintzen; Y Liu
Journal:  EMBO J       Date:  2001-01-15       Impact factor: 11.598

7.  The pro1(+) gene from Sordaria macrospora encodes a C6 zinc finger transcription factor required for fruiting body development.

Authors:  S Masloff; S Pöggeler; U Kück
Journal:  Genetics       Date:  1999-05       Impact factor: 4.562

8.  Genome analysis: Assigning protein coding regions to three-dimensional structures.

Authors:  A A Salamov; M Suwa; C A Orengo; M B Swindells
Journal:  Protein Sci       Date:  1999-04       Impact factor: 6.725

9.  Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils.

Authors:  A E Keating; V N Malashkevich; B Tidor; P S Kim
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-18       Impact factor: 11.205

10.  BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens.

Authors:  P Bradley; L Cowen; M Menke; J King; B Berger
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-18       Impact factor: 11.205
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