Lanczycki Christopher J, Chakrabarti Saikat
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Bioinformation. 2008 Feb 22;2(7):279-83. doi: 10.6026/97320630002279.
Understanding and characterizing the biochemical and evolutionary information within the wealth of protein sequence and structural data, particularly at functionally important sites, is very important. A comprehensive analysis of physico-chemical properties and evolutionary conservation patterns at the molecular and biological function level is expected to yield important clues for identifying similar sites in as-yet uncharacterized proteins. We present a library of protein functional templates (PFTs) designed to represent the compositional and evolutionary conservation patterns of functional sites at the molecular and biological function level. Subsequently we developed LIMACS (LInear MAtching of Conservation Scores), a software tool that uses the template library for the prediction of functionally important sites in a multiple sequence alignment, transferring the molecular function annotation from the most-similar functional site in the template library to a predicted site.
The PFT library, the LIMACS program and source code are available for PC, Mac and Linux operating systems from ftp://ftp.ncbi.nih.gov/pub/lanczyck/limacs.
理解并刻画丰富的蛋白质序列和结构数据中的生化及进化信息，尤其是在功能重要位点的信息，非常重要。在分子和生物学功能水平上对物理化学性质和进化保守模式进行全面分析，有望为识别尚未表征的蛋白质中的相似位点提供重要线索。我们展示了一个蛋白质功能模板（PFT）库，其设计目的是在分子和生物学功能水平上代表功能位点的组成和进化保守模式。随后我们开发了LIMACS（保守得分线性匹配），这是一种软件工具，它使用模板库在多序列比对中预测功能重要位点，将模板库中最相似功能位点的分子功能注释转移到预测位点。
PFT库、LIMACS程序和源代码可从ftp://ftp.ncbi.nih.gov/pub/lanczyck/limacs获取，适用于PC、Mac和Linux操作系统。
