Literature DB >> 19351533

CDF it all: consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions.

Bin Xue1, Christopher J Oldfield, A Keith Dunker, Vladimir N Uversky.   

Abstract

Many biologically active proteins are intrinsically disordered. A reasonable understanding of the disorder status of these proteins may be beneficial for better understanding of their structures and functions. The disorder contents of disordered proteins vary dramatically, with two extremes being fully ordered and fully disordered proteins. Often, it is necessary to perform a binary classification and classify a whole protein as ordered or disordered. Here, an improved error estimation technique was applied to develop the cumulative distribution function (CDF) algorithms for several established disorder predictors. A consensus binary predictor, based on the artificial neural networks, NN-CDF, was developed by using output of the individual CDFs. The consensus method outperforms the individual predictors by 4-5% in the averaged accuracy.

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Year:  2009        PMID: 19351533      PMCID: PMC2683465          DOI: 10.1016/j.febslet.2009.03.070

Source DB:  PubMed          Journal:  FEBS Lett        ISSN: 0014-5793            Impact factor:   4.124


  36 in total

1.  The protein non-folding problem: amino acid determinants of intrinsic order and disorder.

Authors:  R M Williams; Z Obradovi; V Mathura; W Braun; E C Garner; J Young; S Takayama; C J Brown; A K Dunker
Journal:  Pac Symp Biocomput       Date:  2001

Review 2.  What does it mean to be natively unfolded?

Authors:  Vladimir N Uversky
Journal:  Eur J Biochem       Date:  2002-01

Review 3.  Coupling of folding and binding for unstructured proteins.

Authors:  H Jane Dyson; Peter E Wright
Journal:  Curr Opin Struct Biol       Date:  2002-02       Impact factor: 6.809

Review 4.  Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm.

Authors:  P E Wright; H J Dyson
Journal:  J Mol Biol       Date:  1999-10-22       Impact factor: 5.469

Review 5.  Protein folding revisited. A polypeptide chain at the folding-misfolding-nonfolding cross-roads: which way to go?

Authors:  V N Uversky
Journal:  Cell Mol Life Sci       Date:  2003-09       Impact factor: 9.261

Review 6.  Flexible nets. The roles of intrinsic disorder in protein interaction networks.

Authors:  A Keith Dunker; Marc S Cortese; Pedro Romero; Lilia M Iakoucheva; Vladimir N Uversky
Journal:  FEBS J       Date:  2005-10       Impact factor: 5.542

Review 7.  Prediction of protein disorder at the domain level.

Authors:  Zsuzsanna Dosztányi; Márk Sándor; Peter Tompa; István Simon
Journal:  Curr Protein Pept Sci       Date:  2007-04       Impact factor: 3.272

8.  Intrinsic protein disorder in complete genomes.

Authors:  A K Dunker; Z Obradovic; P Romero; E C Garner; C J Brown
Journal:  Genome Inform Ser Workshop Genome Inform       Date:  2000

Review 9.  Intrinsically disordered proteins in human diseases: introducing the D2 concept.

Authors:  Vladimir N Uversky; Christopher J Oldfield; A Keith Dunker
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

10.  Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.

Authors:  J J Ward; J S Sodhi; L J McGuffin; B F Buxton; D T Jones
Journal:  J Mol Biol       Date:  2004-03-26       Impact factor: 5.469

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  56 in total

Review 1.  Understanding protein non-folding.

Authors:  Vladimir N Uversky; A Keith Dunker
Journal:  Biochim Biophys Acta       Date:  2010-02-01

2.  Expanding the proteome: disordered and alternatively folded proteins.

Authors:  H Jane Dyson
Journal:  Q Rev Biophys       Date:  2011-07-01       Impact factor: 5.318

3.  How disordered is my protein and what is its disorder for? A guide through the "dark side" of the protein universe.

Authors:  Philippe Lieutaud; François Ferron; Alexey V Uversky; Lukasz Kurgan; Vladimir N Uversky; Sonia Longhi
Journal:  Intrinsically Disord Proteins       Date:  2016-12-21

4.  A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development.

Authors:  Xiaolin Sun; Bin Xue; William T Jones; Erik Rikkerink; A Keith Dunker; Vladimir N Uversky
Journal:  Plant Mol Biol       Date:  2011-07-06       Impact factor: 4.076

5.  Inherent relationships among different biophysical prediction methods for intrinsically disordered proteins.

Authors:  Fan Jin; Zhirong Liu
Journal:  Biophys J       Date:  2013-01-22       Impact factor: 4.033

6.  Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships.

Authors:  Jianhong Zhou; Christopher J Oldfield; Wenying Yan; Bairong Shen; A Keith Dunker
Journal:  Protein Sci       Date:  2019-08-09       Impact factor: 6.725

Review 7.  Protein intrinsic disorder as a flexible armor and a weapon of HIV-1.

Authors:  Bin Xue; Marcin J Mizianty; Lukasz Kurgan; Vladimir N Uversky
Journal:  Cell Mol Life Sci       Date:  2011-10-28       Impact factor: 9.261

Review 8.  Hydrogen-exchange mass spectrometry for the study of intrinsic disorder in proteins.

Authors:  Deepa Balasubramaniam; Elizabeth A Komives
Journal:  Biochim Biophys Acta       Date:  2012-10-22

9.  Unfoldomics of human diseases: linking protein intrinsic disorder with diseases.

Authors:  Vladimir N Uversky; Christopher J Oldfield; Uros Midic; Hongbo Xie; Bin Xue; Slobodan Vucetic; Lilia M Iakoucheva; Zoran Obradovic; A Keith Dunker
Journal:  BMC Genomics       Date:  2009-07-07       Impact factor: 3.969

10.  Archaic chaos: intrinsically disordered proteins in Archaea.

Authors:  Bin Xue; Robert W Williams; Christopher J Oldfield; A Keith Dunker; Vladimir N Uversky
Journal:  BMC Syst Biol       Date:  2010-05-28
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