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REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding.
BMC Structural Biology Pub Date : 2017-04-24 , DOI: 10.1186/s12900-017-0074-z
Hisashi Mizutani 1 , Hideaki Sugawara 1 , Ashley M Buckle 2 , Takeshi Sangawa 3 , Ken-Ichi Miyazono 4 , Jun Ohtsuka 4 , Koji Nagata 4 , Tomoki Shojima 4 , Shohei Nosaki 4 , Yuqun Xu 4 , Delong Wang 4 , Xiao Hu 4 , Masaru Tanokura 4 , Kei Yura 1, 5, 6, 7
Affiliation  

BACKGROUND More than 7000 papers related to "protein refolding" have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource - "REFOLDdb" that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest. RESULTS We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17th, 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/ . CONCLUSION REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.

中文翻译:

REFOLDdb:一种新的,可持续的通往蛋白重折叠实验方案的途径。

背景技术迄今为止,已经发表了与“蛋白质复性”有关的7000多篇论文,在过去的十年中每年大约有300篇报告。尽管其中一些论文提供了蛋白质重折叠的实验方案,但结构生命科学界的一项调查显示,有必要建立一个全面的重折叠技术数据库。因此,我们开发了一种新的资源-“ REFOLDdb”,它将重新折叠技术收集到一个可搜索的存储库中,以帮助研究人员开发感兴趣蛋白质的重新折叠方案。结果我们的资源基于现有的REFOLD数据库,自2009年以来未进行过更新。我们重新设计了数据格式,使其更加简洁,与原始REFOLD数据库相比,数据条目之间的表示形式保持一致。重塑的数据体系结构提高了搜索效率,并提高了数据库的可持续性。经过详尽的文献搜索后,我们从2009年至2017年初的报告中添加了实验性重新折叠协议。除了这些新数据之外,我们还将现有的REFOLD数据完全转换并集成到了我们的新资源中。截至2017年3月17日,REFOLDdb包含1877个条目,可从http://p4d-info.nig.ac.jp/refolddb/免费获得。结论REFOLDdb是生命科学研究领域的唯一数据库,为设计新的折叠协议和自定义现有方法提供注释信息。我们设想,该资源将在依赖纯净,活性,重组蛋白生产的广泛学科中找到广泛的用途。此外,
更新日期:2017-04-24
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