RUPEE: A fast and accurate purely geometric protein structure search
RUPEE: A fast and accurate purely geometric protein structure search
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DOI：
10.1371/journal.pone.0213712
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发表时间：
2019-03-15
期刊：
影响因子：
3.7
通讯作者：
Lee, Yugyung
中科院分区：
文献类型：
--
作者：
Ayoub, Ronald;Lee, Yugyung
鉴于蛋白质结构和功能之间的密切关系，蛋白质结构搜索长期以来在生物信息学中发挥着既定的作用。尽管已经成熟，现有的蛋白质结构搜索要么使用简化的假设，要么在快速响应时间和结果质量之间进行折衷。这些限制可能会阻碍对蛋白质结构之间关系的简单有效的探索，而这在其他研究领域是常态。为了解决这些限制，我们开发了 RUPEE，一种快速、准确的纯几何结构搜索，它将信息检索和大数据技术与扭转角序列编码的新颖方法相结合。将我们的结果与 mTM、SSM 和 CATHEDRAL 结构扫描的输出进行比较，很明显，RUPEE 为蛋白质结构搜索的纯几何大数据方法设定了新的标准。顶部对齐模式下的 RUPEE 产生的结果与最佳可用蛋白质结构搜索相同或更好，而快速模式下的 RUPEE 则展示了最快的响应时间和高质量的结果。 RUPEE 蛋白质结构搜索可在 https://ayoubresearoh.com 上获取。代码和数据可在 https://github.com/rayoub/rupee 获取。
Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results. These limitations can prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. To address these limitations we have developed RUPEE, a fast and accurate purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles. Comparing our results to the output of mTM, SSM, and the CATHEDRAL structural scan, it is clear that RUPEE has set a new bar for purely geometric big data approaches to protein structure searches. RUPEE in top-aligned mode produces equal or better results than the best available protein structure searches, and RUPEE in fast mode demonstrates the fastest response times coupled with high quality results. The RUPEE protein structure search is available at https://ayoubresearoh.com. Code and data are available at https://github.com/rayoub/rupee.