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Prediction of Intrinsic Disorder with Quality Assessment Using QUARTER

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Protein Structure Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2165))

Abstract

Intrinsically disordered regions (IDRs) are estimated to be highly abundant in nature. While only several thousand proteins are annotated with experimentally derived IDRs, computational methods can be used to predict IDRs for the millions of currently uncharacterized protein chains. Several dozen disorder predictors were developed over the last few decades. While some of these methods provide accurate predictions, unavoidably they also make some mistakes. Consequently, one of the challenges facing users of these methods is how to decide which predictions can be trusted and which are likely incorrect. This practical problem can be solved using quality assessment (QA) scores that predict correctness of the underlying (disorder) predictions at a residue level. We motivate and describe a first-of-its-kind toolbox of QA methods, QUARTER (QUality Assessment for pRotein inTrinsic disordEr pRedictions), which provides the scores for a diverse set of ten disorder predictors. QUARTER is available to the end users as a free and convenient webserver at http://biomine.cs.vcu.edu/servers/QUARTER/. We briefly describe the predictive architecture of QUARTER and provide detailed instructions on how to use the webserver. We also explain how to interpret results produced by QUARTER with the help of a case study.

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Acknowledgments

This research was supported in part by the National Science Foundation grant 1617369 and the Robert J. Mattauch Endowment funds to L.K.

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Authors and Affiliations

  1. School of Mathematical Sciences and LPMC, Nankai University, Tianjin, People’s Republic of China

    Zhonghua Wu

  2. School of Statistics and Data Science, Key Laboratory for Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, People’s Republic of China

    Gang Hu

  3. Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA

    Christopher J. Oldfield

  4. Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA

    Lukasz Kurgan

Authors
  1. Zhonghua Wu
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  2. Gang Hu
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  3. Christopher J. Oldfield
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  4. Lukasz Kurgan
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Correspondence to Lukasz Kurgan .

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Editors and Affiliations

  1. Department of Computer Science, Purdue University, West Lafayette, IN, USA

    Daisuke Kihara

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Wu, Z., Hu, G., Oldfield, C.J., Kurgan, L. (2020). Prediction of Intrinsic Disorder with Quality Assessment Using QUARTER. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 2165. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0708-4_5

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  • DOI: https://doi.org/10.1007/978-1-0716-0708-4_5

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