Suppr超能文献

CASP10中蛋白质无序区域预测的评估

Assessment of protein disorder region predictions in CASP10.

作者信息

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

机构信息

Genome Center University of California, Davis, Davis, California, 95616.

出版信息

Proteins. 2014 Feb;82 Suppl 2(0 2):127-37. doi: 10.1002/prot.24391. Epub 2013 Nov 22.

Abstract

The article presents the assessment of disorder region predictions submitted to CASP10. The evaluation is based on the three measures tested in previous CASPs: (i) balanced accuracy, (ii) the Matthews correlation coefficient for the binary predictions, and (iii) the area under the curve in the receiver operating characteristic (ROC) analysis of predictions using probability annotation. We also performed new analyses such as comparison of the submitted predictions with those obtained with a Naïve disorder prediction method and with predictions from the disorder prediction databases D2P2 and MobiDB. On average, the methods participating in CASP10 demonstrated slightly better performance than those in CASP9.

摘要

本文介绍了对提交给CASP10的无序区域预测的评估。评估基于在前几届CASP中测试的三种指标:(i) 平衡准确率,(ii) 二元预测的马修斯相关系数,以及(iii) 使用概率注释的预测在接受者操作特征(ROC)分析中的曲线下面积。我们还进行了新的分析,例如将提交的预测与使用简单无序预测方法获得的预测以及与来自无序预测数据库D2P2和MobiDB的预测进行比较。平均而言,参与CASP10的方法表现略优于CASP9中的方法。

相似文献

1
Assessment of protein disorder region predictions in CASP10.
Proteins. 2014 Feb;82 Suppl 2(0 2):127-37. doi: 10.1002/prot.24391. Epub 2013 Nov 22.
2
Evaluation of disorder predictions in CASP9.
Proteins. 2011;79 Suppl 10(S10):107-18. doi: 10.1002/prot.23161. Epub 2011 Sep 16.
3
Evaluation of residue-residue contact prediction in CASP10.
Proteins. 2014 Feb;82 Suppl 2(0 2):138-53. doi: 10.1002/prot.24340. Epub 2013 Aug 31.
4
Exploring Protein Intrinsic Disorder with MobiDB.
Methods Mol Biol. 2020;2141:127-143. doi: 10.1007/978-1-0716-0524-0_6.
5
Computational Prediction of Intrinsic Disorder in Proteins.
Curr Protoc Protein Sci. 2017 Apr 3;88:2.16.1-2.16.14. doi: 10.1002/cpps.28.
6
Predicting Conformational Disorder.
Methods Mol Biol. 2016;1415:265-99. doi: 10.1007/978-1-4939-3572-7_14.
7
Assessment of the assessment: evaluation of the model quality estimates in CASP10.
Proteins. 2014 Feb;82 Suppl 2(0 2):112-26. doi: 10.1002/prot.24347. Epub 2013 Aug 31.
8
CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL.
Proteins. 2014 Feb;82 Suppl 2(0 2):7-13. doi: 10.1002/prot.24399. Epub 2013 Oct 18.
10
Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus.
J Biomol Struct Dyn. 2014;32(3):448-64. doi: 10.1080/07391102.2013.775969. Epub 2013 Mar 27.

引用本文的文献

1
Evaluation of predictions of disordered binding regions in the CAID2 experiment.
Comput Struct Biotechnol J. 2024 Dec 17;27:78-88. doi: 10.1016/j.csbj.2024.12.009. eCollection 2025.
2
Accurate and Fast Prediction of Intrinsic Disorder Using flDPnn.
Methods Mol Biol. 2025;2867:201-218. doi: 10.1007/978-1-0716-4196-5_12.
3
Assessment of Disordered Linker Predictions in the CAID2 Experiment.
Biomolecules. 2024 Feb 28;14(3):287. doi: 10.3390/biom14030287.
4
Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins.
Nat Protoc. 2023 Nov;18(11):3157-3172. doi: 10.1038/s41596-023-00876-x. Epub 2023 Sep 22.
5
Development of a candidate multi-epitope vaccine against : Reverse vaccinology and immunoinformatics approach.
Saudi Med J. 2023 Jun;44(6):544-559. doi: 10.15537/smj.2023.44.6.20220733.
6
DEPICTER2: a comprehensive webserver for intrinsic disorder and disorder function prediction.
Nucleic Acids Res. 2023 Jul 5;51(W1):W141-W147. doi: 10.1093/nar/gkad330.
7
Computational Methods to Predict Intrinsically Disordered Regions and Functional Regions in Them.
Methods Mol Biol. 2023;2627:231-245. doi: 10.1007/978-1-0716-2974-1_13.
8
Computational prediction of disordered binding regions.
Comput Struct Biotechnol J. 2023 Feb 10;21:1487-1497. doi: 10.1016/j.csbj.2023.02.018. eCollection 2023.
10
SETH predicts nuances of residue disorder from protein embeddings.
Front Bioinform. 2022 Oct 10;2:1019597. doi: 10.3389/fbinf.2022.1019597. eCollection 2022.

本文引用的文献

1
Definition and classification of evaluation units for CASP10.
Proteins. 2014 Feb;82 Suppl 2(0 2):14-25. doi: 10.1002/prot.24434. Epub 2013 Nov 22.
2
CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL.
Proteins. 2014 Feb;82 Suppl 2(0 2):7-13. doi: 10.1002/prot.24399. Epub 2013 Oct 18.
3
Assessment of the assessment: evaluation of the model quality estimates in CASP10.
Proteins. 2014 Feb;82 Suppl 2(0 2):112-26. doi: 10.1002/prot.24347. Epub 2013 Aug 31.
4
A decade and a half of protein intrinsic disorder: biology still waits for physics.
Protein Sci. 2013 Jun;22(6):693-724. doi: 10.1002/pro.2261. Epub 2013 Apr 29.
5
The contribution of intrinsic disorder prediction to the elucidation of protein function.
Curr Opin Struct Biol. 2013 Jun;23(3):467-72. doi: 10.1016/j.sbi.2013.02.001. Epub 2013 Mar 1.
6
Protein flexibility, not disorder, is intrinsic to molecular recognition.
F1000 Biol Rep. 2013;5:2. doi: 10.3410/B5-2. Epub 2013 Jan 11.
8
Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding.
Protein Sci. 2013 Mar;22(3):258-73. doi: 10.1002/pro.2207. Epub 2013 Jan 27.
9
Utilization of protein intrinsic disorder knowledge in structural proteomics.
Biochim Biophys Acta. 2013 Feb;1834(2):487-98. doi: 10.1016/j.bbapap.2012.12.003. Epub 2012 Dec 8.
10
D²P²: database of disordered protein predictions.
Nucleic Acids Res. 2013 Jan;41(Database issue):D508-16. doi: 10.1093/nar/gks1226. Epub 2012 Nov 29.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验