IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0004433.html
   My bibliography  Save this article

Improved Disorder Prediction by Combination of Orthogonal Approaches

Author

Listed:
  • Avner Schlessinger
  • Marco Punta
  • Guy Yachdav
  • Laszlo Kajan
  • Burkhard Rost

Abstract

Disordered proteins are highly abundant in regulatory processes such as transcription and cell-signaling. Different methods have been developed to predict protein disorder often focusing on different types of disordered regions. Here, we present MD, a novel META-Disorder prediction method that molds various sources of information predominantly obtained from orthogonal prediction methods, to significantly improve in performance over its constituents. In sustained cross-validation, MD not only outperforms its origins, but it also compares favorably to other state-of-the-art prediction methods in a variety of tests that we applied. Availability: http://www.rostlab.org/services/md/

Suggested Citation

  • Avner Schlessinger & Marco Punta & Guy Yachdav & Laszlo Kajan & Burkhard Rost, 2009. "Improved Disorder Prediction by Combination of Orthogonal Approaches," PLOS ONE, Public Library of Science, vol. 4(2), pages 1-10, February.
  • Handle: RePEc:plo:pone00:0004433
    DOI: 10.1371/journal.pone.0004433
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004433
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0004433&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0004433?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Kenji Sugase & H. Jane Dyson & Peter E. Wright, 2007. "Mechanism of coupled folding and binding of an intrinsically disordered protein," Nature, Nature, vol. 447(7147), pages 1021-1025, June.
    2. Avner Schlessinger & Jinfeng Liu & Burkhard Rost, 2007. "Natively Unstructured Loops Differ from Other Loops," PLOS Computational Biology, Public Library of Science, vol. 3(7), pages 1-12, July.
    3. Jenny Gu & Michael Gribskov & Philip E Bourne, 2006. "Wiggle—Predicting Functionally Flexible Regions from Primary Sequence," PLOS Computational Biology, Public Library of Science, vol. 2(7), pages 1-17, July.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Esmeralda Vicedo & Avner Schlessinger & Burkhard Rost, 2015. "Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-21, August.
    2. Jiangning Song & Hao Tan & Mingjun Wang & Geoffrey I Webb & Tatsuya Akutsu, 2012. "TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-16, February.
    3. Zhiheng Wang & Qianqian Yang & Tonghua Li & Peisheng Cong, 2015. "DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-16, June.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Iskra Staneva & Yongqi Huang & Zhirong Liu & Stefan Wallin, 2012. "Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study," PLOS Computational Biology, Public Library of Science, vol. 8(9), pages 1-9, September.
    2. Wenzhe Liu & Limin Chen & Dongbao Yin & Zhiheng Yang & Jianfei Feng & Qi Sun & Luhua Lai & Xuefeng Guo, 2023. "Visualizing single-molecule conformational transition and binding dynamics of intrinsically disordered proteins," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Michael Knott & Robert B Best, 2012. "A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-10, July.
    4. Esmeralda Vicedo & Avner Schlessinger & Burkhard Rost, 2015. "Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-21, August.
    5. Jiangning Song & Hao Tan & Mingjun Wang & Geoffrey I Webb & Tatsuya Akutsu, 2012. "TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-16, February.
    6. Kalyan S. Chakrabarti & Simon Olsson & Supriya Pratihar & Karin Giller & Kerstin Overkamp & Ko On Lee & Vytautas Gapsys & Kyoung-Seok Ryu & Bert L. Groot & Frank Noé & Stefan Becker & Donghan Lee & Th, 2022. "A litmus test for classifying recognition mechanisms of transiently binding proteins," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    7. Jiangning Song & Hao Tan & Andrew J Perry & Tatsuya Akutsu & Geoffrey I Webb & James C Whisstock & Robert N Pike, 2012. "PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-23, November.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0004433. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.