Assessment of protein disorder region predictions in CASP10

Monastyrskyy, Bohdan; Kryshtafovych, Andriy; Moult, John; Tramontano, Anna; Fidelis, Krzysztof

doi:10.1002/prot.24391

Cited by 154 publications

(189 citation statements)

References 39 publications

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“…This is evident when comparing the results of several recent comparative assessments. 12,79,80 In spite of the fact these studies point to certain methods are being more accurate than other methods, they do not agree on which specific method is the most accurate. In addition, many of these predictors achieve similar goals.…”

Section: Running Disorder Predictionsmentioning

confidence: 93%

“…In CASP10 (2012), the last CASP that included assessment of predictions of disorder, the top 3 predictors were PrDOS, DISOPRED, and MFDp. 12 Their results were shown to be statistically better than the remaining 23 predictors. 12 Their results were also shown to improve with the increase of the disorder region length cutoff from 4 to 20 to 30 residue-long segments.…”

Section: Running Disorder Predictionsmentioning

confidence: 95%

“…The availability of different types of predictors allows users to select various aspects of disorder prediction that are suitable to their current studies, and choose an appropriate predictor. 12 It has also been shown that, since different disorder predictors are based on different definitions of disorder, combining several predictions from different predictors reinforces the reliability of the overall predictions on a specific position or region. [81][82][83][84] This reasoning has given rise to the development of metapredictors, which help users deal with the growing number of available disorder predictors and typically improve accuracy by combining the results of several different predictors.…”

Section: Introductionmentioning

confidence: 93%

“…the database of experimentally validated IDPs/IDPRs, see below), 11 is 5 residues, and the minimal length of 4 residues was used to annotate disordered regions used in the CASP experiments. 12,13 In protein science, the existence of intrinsic disorder in proteins has been known for a long time. This is in spite of the fact that it contradicts the classical protein sequence-structure-function paradigm where the "lock-and-key" model is used to explain how a protein can achieve its biological function via folding into a unique, highly structured state determined by its amino acid sequence.…”

Section: Introductionmentioning

confidence: 99%

“…12,69,71,[76][77][78][79][80]. The availability of different types of predictors allows users to select various aspects of disorder prediction that are suitable to their current studies, and choose an appropriate predictor.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

How disordered is my protein and what is its disorder for? A guide through the “dark side” of the protein universe

Lieutaud

Ferrón

Uversky

et al. 2016

Intrinsically Disordered Proteins

104

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In the last 2 decades it has become increasingly evident that a large number of proteins are either fully or partially disordered. Intrinsically disordered proteins lack a stable 3D structure, are ubiquitous and fulfill essential biological functions. Their conformational heterogeneity is encoded in their amino acid sequences, thereby allowing intrinsically disordered proteins or regions to be recognized based on properties of these sequences. The identification of disordered regions facilitates the functional annotation of proteins and is instrumental for delineating boundaries of protein domains amenable to structural determination with X-ray crystallization. This article discusses a comprehensive selection of databases and methods currently employed to disseminate experimental and putative annotations of disorder, predict disorder and identify regions involved in induced folding. It also provides a set of detailed instructions that should be followed to perform computational analysis of disorder.KEYWORDS disorder databases and metaservers; induced folding; intrinsic disorder; intrinsically disordered proteins; intrinsically disordered regions; prediction methods

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Section: Running Disorder Predictionsmentioning

confidence: 93%

Section: Running Disorder Predictionsmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

How disordered is my protein and what is its disorder for? A guide through the “dark side” of the protein universe

Lieutaud

Ferrón

Uversky

et al. 2016

Intrinsically Disordered Proteins

104

View full text Add to dashboard Cite

show abstract

Biophysical characterisation of the recombinant human frataxin precursor

et al. 2018

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Friedreich's ataxia is a disease caused by a decrease in the levels of expression or loss of functionality of the mitochondrial protein frataxin ( FXN ). The development of an active and stable recombinant variant of FXN is important for protein replacement therapy. Although valuable data about the mature form FXN 81‐210 has been collected, not enough information is available about the conformation of the frataxin precursor ( FXN 1‐210). We investigated the conformation, stability and function of a recombinant precursor variant (His6‐ TAT ‐ FXN 1‐210), which includes a TAT peptide in the N‐terminal region to assist with transport across cell membranes. His6‐ TAT ‐ FXN 1‐210 was expressed in Escherichia coli and conditions were found for purifying folded protein free of aggregation, oxidation or degradation, even after freezing and thawing. The protein was found to be stable and monomeric, with the N‐terminal stretch (residues 1–89) mostly unstructured and the C‐terminal domain properly folded. The experimental data suggest a complex picture for the folding process of full‐length frataxin in vitro : the presence of the N‐terminal region increased the tendency of FXN to aggregate at high temperatures but this could be avoided by the addition of low concentrations of GdmCl. The purified precursor was translocated through cell membranes. In addition, immune response against His6‐ TAT ‐ FXN 1‐210 was measured, suggesting that the C‐terminal fragment was not immunogenic at the assayed protein concentrations. Finally, the recognition of recombinant FXN by cellular proteins was studied to evaluate its functionality. In this regard, cysteine desulfurase NFS 1/ ISD 11/ ISCU was activated in vitro by His6‐ TAT ‐ FXN 1‐210. Moreover, the results showed that His6‐ TAT ‐ FXN 1‐210 can be ubiquitinated in vitro by the recently identified frataxin E3 ligase RNF 126, in a similar way as the FXN 1‐210, suggesting that the His6‐ TAT extension does not interfere with the ubiquitination machinery.

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Protein Structure Prediction

Roy

Zhang

2012

Encyclopedia of Life Sciences

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Predicting 3D structure of protein from its amino acid sequence is one of the most important unsolved problems in biophysics and computational biology. This paper attempts to give a comprehensive introduction of the most recent effort and progress on protein structure prediction. Following the general flowchart of structure prediction, related concepts and methods are presented and discussed. Moreover, brief introductions are made to several widely-used prediction methods and the community-wide critical assessment of protein structure prediction (CASP) experiments.

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Assessment of protein disorder region predictions in CASP10

Cited by 154 publications

References 39 publications

How disordered is my protein and what is its disorder for? A guide through the “dark side” of the protein universe

How disordered is my protein and what is its disorder for? A guide through the “dark side” of the protein universe

Biophysical characterisation of the recombinant human frataxin precursor

Protein Structure Prediction

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