Exploiting heterogeneous sequence properties improves prediction of protein disorder

Proteins
Zoran ObradovicA Keith Dunker

Abstract

During the past few years we have investigated methods to improve predictors of intrinsically disordered regions longer than 30 consecutive residues. Experimental evidence, however, showed that these predictors were less successful on short disordered regions, as observed two years ago during the fifth Critical Assessment of Techniques for Protein Structure Prediction (CASP5). To address this shortcoming, we developed a two-level model called VSL1 (CASP6 id: 193-1). At the first level, VSL1 consists of two specialized predictors, one of which was optimized for long disordered regions (>30 residues) and the other for short disordered regions (< or =30 residues). At the second level, a meta-predictor was built to assign weights for combining the two first-level predictors. As the results of the CASP6 experiment showed, this new predictor has achieved the highest accuracy yet and significantly improved performance on short disordered regions, while maintaining high performance on long disordered regions.

References

Jun 1, 1994·Proteins·M VihinenP Riikonen
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Nov 5, 1999·Journal of Molecular Biology·P E Wright, H J Dyson
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Nov 28, 2000·Proteins·P RomeroA K Dunker
May 31, 2001·Journal of Molecular Graphics & Modelling·A K DunkerZ Obradovic
Jan 11, 2002·European Journal of Biochemistry·Vladimir N Uversky
May 23, 2002·Biochemistry·A Keith DunkerZoran Obradović
Oct 9, 2002·Trends in Biochemical Sciences·Peter Tompa
Oct 17, 2002·Journal of Molecular Biology·Lilia M IakouchevaA Keith Dunker
Nov 7, 2002·Advances in Protein Chemistry·A Keith DunkerZoran Obradovic
Dec 14, 2002·Annals of the New York Academy of Sciences·Rose Anne M KennyClive Ballard
Apr 30, 2003·Protein Science : a Publication of the Protein Society·David K SmithGuang Zhu
Jun 26, 2003·Nucleic Acids Research·Rune LindingToby J Gibson
Jun 26, 2003·Nucleic Acids Research·Jinfeng Liu, Burkhard Rost
Aug 12, 2003·Proteins·Slobodan VuceticZoran Obradovic
Oct 28, 2003·Proteins·Eugene Melamud, John Moult
Oct 28, 2003·Proteins·Zoran ObradovicA Keith Dunker
Nov 8, 2003·Structure·Rune LindingRobert B Russell
Dec 24, 2003·Protein Science : a Publication of the Protein Society·Predrag RadivojacA Keith Dunker
Jul 21, 2004·Journal of Structural and Functional Genomics·Wolfgang PetiKurt Wüthrich
Jul 31, 2004·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Peter Tompa, Peter Csermely
Aug 18, 2004·Bioinformatics·Slobodan VuceticA Keith Dunker
Oct 7, 2004·Current Opinion in Structural Biology·Clay BrackenA Keith Dunker
Dec 21, 2004·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant
Jan 20, 2005·Bioinformatics·Karen Coeytaux, Anne Poupon
Feb 9, 2005·Biochemistry·Christopher J OldfieldA Keith Dunker
Mar 2, 2005·Nature Reviews. Molecular Cell Biology·H Jane Dyson, Peter E Wright
Mar 8, 2005·Journal of Bioinformatics and Computational Biology·Kang PengZoran Obradovic
Mar 25, 2005·Proteins·Christopher J OldfieldJohn L Markley
Sep 28, 2005·Proteins·Yumi Jin, Roland L Dunbrack

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Citations

Aug 18, 2010·Cellular and Molecular Life Sciences : CMLS·Muralidhar L HegdeSankar Mitra
Jun 1, 2006·Biochemistry·Jiangang LiuA Keith Dunker
May 10, 2007·Journal of Proteome Research·Vladimir VacicA Keith Dunker
Jan 26, 2010·Journal of Proteome Research·Ekaterina PosokhovaKirill A Martemyanov
Jul 15, 2009·Cell Research·Bo HeA Keith Dunker
Jun 15, 2010·Molecular BioSystems·Jessica H Fong, Anna R Panchenko
Apr 21, 2010·Proceedings of the National Academy of Sciences of the United States of America·Albert H MaoRohit V Pappu
Jun 2, 2011·Proceedings of the National Academy of Sciences of the United States of America·Jorge A LamboyElizabeth A Komives
Apr 28, 2009·The Journal of Biological Chemistry·Nathalie SelevsekHans W Adolph
Jan 20, 2011·The Journal of Biological Chemistry·Lisa M SeymourMark J Walker
Jun 26, 2008·The Journal of Biological Chemistry·Matthew J FooterJulie A Theriot
Sep 10, 2008·The Journal of Biological Chemistry·Svend HaaningJens Stougaard
Dec 25, 2008·The Journal of Biological Chemistry·Quinn K Kleerekoper, John A Putkey
Aug 13, 2010·Molecular & Cellular Proteomics : MCP·Jianjiong GaoDong Xu
Mar 6, 2012·Molecular & Cellular Proteomics : MCP·Roberto MoscaPatrick Aloy
Jan 3, 2012·Journal of Biomolecular Structure & Dynamics·Tuo ZhangYaoqi Zhou
Jan 24, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Pengfei HanZhi-Ping Feng
Jan 18, 2012·Genome Biology and Evolution·Anna R KerstingSonja Grath
Jun 13, 2012·Nucleic Acids Research·Alexandre G de BrevernJean-Christophe Gelly
Oct 13, 2009·Genome Research·Ariel Fernández, Jianping Chen
Mar 25, 2010·Biochemistry. Biokhimii︠a︡·O M SelivanovaI N Serdyuk
Dec 23, 2009·BMC Bioinformatics·Xin DengJianlin Cheng
Jan 9, 2009·BMC Bioinformatics·Pengfei HanZhi-Ping Feng
Feb 28, 2009·BMC Bioinformatics·Pengfei HanZhi-Ping Feng
Jun 30, 2012·BMC Bioinformatics·Joanna M KasprzakJanusz M Bujnicki
Mar 19, 2013·BMC Bioinformatics·Jesse Eickholt, Jianlin Cheng
Apr 19, 2006·BMC Bioinformatics·Kang PengZoran Obradovic
Jul 25, 2009·BMC Genomics·Vladimir N UverskyA Keith Dunker
Dec 22, 2010·BMC Genomics·Yizhen JiaDavid K Smith
Apr 17, 2008·BMC Genomics·Joshua HeckerJianlin Cheng
Oct 10, 2008·BMC Genomics·Philippe LieutaudSonia Longhi
Feb 16, 2011·BMC Structural Biology·Gabriela V MeirellesJörg Kobarg
Feb 18, 2009·Virology Journal·Eugénie HébrardDenis Fargette

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