School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
Proteins. 2011 Jan;79(1):165-78. doi: 10.1002/prot.22870.
Site-directed mutagenesis is routinely used in modern biology to elucidate the functional or biophysical roles of protein residues, and plays an important role in the field of rational protein design. Over the past decade, a number of computational tools have been developed that can predict the effect of point mutations on a protein's biophysical characteristics. However, these programs usually provide predictions for only a single characteristic. Furthermore, online versions of these tools are often impractical to use for examination of large and diverse sets of mutants. We have created a new web application, (http://enzyme.ucd.ie/PEAT_SA), that can simultaneously predict the effect of mutations on stability, ligand affinity and pK(a) values. PEAT-SA also provides an expanded feature-set with respect to other online tools which includes the ability to obtain predictions for multiple mutants in one submission. As a result, researchers who use site-directed mutagenesis can access state-of-the-art protein design methods with a fraction of the effort previously required. The results of benchmarking PEAT-SA on standard test-sets demonstrate that its accuracy for all three prediction types compares well to currently available tools. We illustrate PEAT-SA's potential by using it to investigate the influence of mutations on the activity of Subtilisin BPN'. This example demonstrates how the ability to obtain a wide range of information from one source, that can be combined to obtain deeper insight into the influence of mutations, makes PEAT-SA a valuable service to both experimental and computational biologists.
定点突变在现代生物学中被广泛应用于阐明蛋白质残基的功能或生物物理作用，并在理性蛋白质设计领域发挥着重要作用。在过去的十年中，已经开发出许多计算工具，可以预测点突变对蛋白质生物物理特性的影响。然而，这些程序通常只能预测单一特性的影响。此外，这些工具的在线版本通常对于检查大量和多样化的突变体来说并不实用。我们创建了一个新的网络应用程序，（http://enzyme.ucd.ie/PEAT_SA），它可以同时预测突变对稳定性、配体亲和力和 pK(a)值的影响。PEAT-SA 还提供了比其他在线工具更扩展的功能集，包括在一次提交中获得多个突变体预测的能力。因此，使用定点突变的研究人员可以以以前所需的一小部分努力来访问最先进的蛋白质设计方法。在标准测试集上对 PEAT-SA 进行基准测试的结果表明，它在所有三种预测类型上的准确性都与当前可用的工具相当。我们通过使用它来研究突变对枯草杆菌蛋白酶 BPN'活性的影响来说明 PEAT-SA 的潜力。这个例子说明了从一个来源获得广泛信息的能力，以及将这些信息结合起来以更深入地了解突变的影响，使得 PEAT-SA 成为实验和计算生物学家都非常有价值的服务。
