Daisy: An integrated repeat protein curation service

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology Pub Date : 2023-10-03 DOI:10.1016/j.jsb.2023.108033

Manuel Bezerra-Brandao, Ronaldo Romario Tunque Cahui, Layla Hirsh

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引用次数: 0

Abstract

Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for protein structure prediction and repeat classification that are useful for this process. However, no service contemplates required databases and software to supplement researching on repeat proteins. In this publication we present Daisy, an integrated repeat protein curation web service. This service can process Protein Data Bank (PDB) and the AlphaFold Database entries for tandem repeats identification. In addition, it uses an algorithm to search a sequence against a library of Pfam hidden Markov model (HMM). Repeat classifications are associated with the identified families through RepeatsDB. This prediction is considered for enhancing the ReUPred algorithm execution and hastening the repeat units identification process. The service can also operate every associated PDB and AlphaFold structure with a UniProt proteome registry.

Availability: The Daisy web service is freely accessible at daisy.bioinformatica.org.

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黛西：一个完整的重复蛋白质管理服务。

蛋白质识别、分类和管理中的串联重复是一个复杂的过程，需要专家的手动处理、处理能力和时间。将机器学习应用于蛋白质结构预测和重复分类的最新相关进展对这一过程很有用。然而，没有任何服务考虑所需的数据库和软件来补充对重复蛋白的研究。在这份出版物中，我们介绍了Daisy，一个集成的重复蛋白质管理网络服务。该服务可以处理蛋白质数据库（PDB）和AlphaFold数据库条目，用于串联重复序列识别。此外，它还使用一种算法来根据Pfam隐马尔可夫模型（HMM）库搜索序列。重复分类通过RepeatsDB与已识别的族相关联。该预测被认为是为了增强ReUPred算法的执行并加快重复单元识别过程。该服务还可以通过UniProt蛋白质组注册表操作每个相关的PDB和AlphaFold结构。可用性：Daisy.bioinformatica.org上可以免费访问Daisy网络服务。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of structural biology 生物-生化与分子生物学

CiteScore

6.30

自引率

3.30%

发文量

审稿时长

65 days

期刊介绍： Journal of Structural Biology (JSB) has an open access mirror journal, the Journal of Structural Biology: X (JSBX), sharing the same aims and scope, editorial team, submission system and rigorous peer review. Since both journals share the same editorial system, you may submit your manuscript via either journal homepage. You will be prompted during submission (and revision) to choose in which to publish your article. The editors and reviewers are not aware of the choice you made until the article has been published online. JSB and JSBX publish papers dealing with the structural analysis of living material at every level of organization by all methods that lead to an understanding of biological function in terms of molecular and supermolecular structure. Techniques covered include: • Light microscopy including confocal microscopy • All types of electron microscopy • X-ray diffraction • Nuclear magnetic resonance • Scanning force microscopy, scanning probe microscopy, and tunneling microscopy • Digital image processing • Computational insights into structure