The value of protein structure classification information-Surveying the scientific literature.
The value of protein structure classification information-Surveying the scientific literature.
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DOI：
10.1002/prot.24915
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发表时间：
2015-11
期刊：
影响因子：
2.9
通讯作者：
Chandonia JM
中科院分区：
文献类型：
--
作者：
Fox NK;Brenner SE;Chandonia JM
蛋白质结构分类（SCOP）和类、结构、拓扑、同源（CATH）数据库已经成为蛋白质结构分类的宝贵资源超过20年。SCOP（第1版）的开发工作于2009年6月完成，SCOP为1.75。SCOPe（SCOP-extended）数据库提供了经典SCOP层次结构的持续发展，增加了33，000多个结构。我们试图评估这20年历史的资源的影响，并指导未来的发展。为此，我们调查了最近的文章，以了解如何使用结构分类数据。在2012-2013年发表的571篇引用SCOP的文章中，439篇实际使用了该资源的数据。我们发现，使用类型在四个主要类别中分布相当均匀：A）研究蛋白质结构或进化（27%的文章），B）训练和/或基准算法（28%的文章），C）使用SCOP分类来增强非SCOP数据集（21%的文章），以及D）检查一种蛋白质/一小组蛋白质的分类（22%的文章）。大多数文章描述了计算研究，尽管11%描述了纯实验研究，还有9%包括两者。我们研究了如何在引用两个数据库的158篇文章中使用CATH和SCOP：虽然一些研究只使用一个数据集，但大多数使用来自两个资源的数据。蛋白质结构分类仍然高度相关的各种各样的问题和设置。蛋白质2015; 83：2025-2038。© 2015作者。蛋白质：结构，功能和生物信息学出版的威利期刊，公司。
The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP–extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012–2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non‐SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings. Proteins 2015; 83:2025–2038. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.