Bioinformatic Analysis Group - GABi, Centro de Investigación y Desarrollo en Biotecnología, Bogotá DC, Colombia.
Brief Bioinform. 2012 May;13(3):329-36. doi: 10.1093/bib/bbr052. Epub 2011 Sep 19.
In recent years, numerous biocomputational tools have been designed to extract functional and evolutionary information from multiple sequence alignments (MSAs) of proteins and genes. Most biologists working actively on the characterization of proteins from a single or family perspective use the MSA analysis to retrieve valuable information about amino acid conservation and the functional role of residues in query protein(s). In MSAs, adjustment of alignment parameters is a key point to improve the quality of MSA output. However, this issue is frequently underestimated and/or misunderstood by scientists and there is no in-depth knowledge available in this field. This brief review focuses on biocomputational approaches complementary to MSA to help distinguish functional residues in protein families. These additional analyses involve issues ranging from phylogenetic to statistical, which address the detection of amino acids pivotal for protein function at any level. In recent years, a large number of tools has been designed for this very purpose. Using some of these relevant, useful tools, we have designed a practical pipeline to perform in silico studies with a view to improving the characterization of family proteins and their functional residues. This review-guide aims to present biologists a set of specially designed tools to study proteins. These tools are user-friendly as they use web servers or easy-to-handle applications. Such criteria are essential for this review as most of the biologists (experimentalists) working in this field are unfamiliar with these biocomputational analysis approaches.
近年来，已经设计了许多生物计算工具，以从蛋白质和基因的多重序列比对（MSA）中提取功能和进化信息。大多数从单个或家族角度积极研究蛋白质特征的生物学家使用 MSA 分析来检索有关氨基酸保守性和查询蛋白质中残基的功能作用的有价值信息。在 MSA 中，调整比对参数是提高 MSA 输出质量的关键。然而，科学家们经常低估和/或误解这个问题，并且在这个领域没有深入的知识。这篇简要综述侧重于补充 MSA 的生物计算方法，以帮助区分蛋白质家族中的功能残基。这些额外的分析涉及从系统发生学到统计的问题，这些问题涉及在任何级别检测对蛋白质功能至关重要的氨基酸。近年来，已经设计了大量的工具来实现这一目标。使用其中一些相关的、有用的工具，我们设计了一个实用的管道来进行计算机模拟研究，以期改进对家族蛋白及其功能残基的特征描述。本综述指南旨在为生物学家提供一套专门设计的工具来研究蛋白质。这些工具使用户友好，因为它们使用网络服务器或易于处理的应用程序。由于该领域的大多数生物学家（实验者）不熟悉这些生物计算分析方法，因此这些标准对于本综述至关重要。
