Leader David P, Milner-White E James
Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
BMC Bioinformatics. 2009 Feb 11;10:60. doi: 10.1186/1471-2105-10-60.
Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are alphabeta-motifs, asx-motifs, asx-turns, beta-bulges, beta-bulge loops, beta-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this.
The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs.
Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema.
小环状基序是蛋白质三维结构的常见组成部分。通常它们由三到七个氨基酸残基组成，并由二面角和氢键结合伙伴的组合来定义。其中最丰富的是αβ基序、asx基序、asx转角、β凸起、β凸起环、β转角、巢状结构、壁龛、谢尔曼环、ST基序、ST钉和ST转角。我们从一系列高质量蛋白质结构中构建了这样一个基序数据库，并构建了一个网络应用程序作为其可视化界面。
网络应用程序Motivated Proteins可访问一个包含400多种代表性蛋白质的数据库中的这12种基序（有48个子类别）。可以针对特定的基序类别或子类别、配体附近的基序、包含酶活性位点一部分的基序、重叠基序或包含特定氨基酸序列的基序进行查询。可以指定单个蛋白质，或者在适当的情况下，查询列出的所有蛋白质的基序。查询结果以文本形式呈现为一个（X）HTML表格，并且可以保存为可解析的纯文本或XML。基序可以在Jmol applet结构查看器中单独查看和操作，也可以在蛋白质的背景下查看和操作。还提供了叠加在蛋白质二级结构线性表示上的基序卡通图。提供了基序的摘要信息、氨基酸分布直方图以及基序中各个位置的二面角图。
Motivated Proteins是一个可公开免费访问的网络应用程序，它使蛋白质科学家能够研究小的三维基序，而无需了解结构化查询语言或底层数据库模式。
