Kelley Lawrence A, Sternberg Michael J E
Structural Bioinformatics Group, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK.
Nat Protoc. 2009;4(3):363-71. doi: 10.1038/nprot.2009.2.
Determining the structure and function of a novel protein is a cornerstone of many aspects of modern biology. Over the past decades, a number of computational tools for structure prediction have been developed. It is critical that the biological community is aware of such tools and is able to interpret their results in an informed way. This protocol provides a guide to interpreting the output of structure prediction servers in general and one such tool in particular, the protein homology/analogy recognition engine (Phyre). New profile-profile matching algorithms have improved structure prediction considerably in recent years. Although the performance of Phyre is typical of many structure prediction systems using such algorithms, all these systems can reliably detect up to twice as many remote homologies as standard sequence-profile searching. Phyre is widely used by the biological community, with >150 submissions per day, and provides a simple interface to results. Phyre takes 30 min to predict the structure of a 250-residue protein.
确定一种新蛋白质的结构和功能是现代生物学诸多方面的基石。在过去几十年里，已经开发出了许多用于结构预测的计算工具。至关重要的是，生物界要了解这些工具，并能够以明智的方式解读其结果。本方案总体上提供了一个解读结构预测服务器输出结果的指南，尤其针对一种这样的工具——蛋白质同源/类似物识别引擎（Phyre）。近年来，新的profile-profile匹配算法显著改进了结构预测。尽管Phyre的性能在许多使用此类算法的结构预测系统中很典型，但所有这些系统能够可靠检测到的远源同源性数量是标准序列-profile搜索的两倍之多。Phyre被生物界广泛使用，每天有超过150次提交，并提供了一个简单的结果界面。Phyre预测一个含250个残基的蛋白质的结构需要30分钟。
