Bennett Steven P, Lu Lin, Brutlag Douglas L
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.
Nucleic Acids Res. 2003 Jul 1;31(13):3328-32. doi: 10.1093/nar/gkg564.
Computational methods such as sequence alignment and motif construction are useful in grouping related proteins into families, as well as helping to annotate new proteins of unknown function. These methods identify conserved amino acids in protein sequences, but cannot determine the specific functional or structural roles of conserved amino acids without additional study. In this work, we present 3MATRIX (http://3matrix.stanford.edu) and 3MOTIF (http://3motif.stanford.edu), a web-based sequence motif visualization system that displays sequence motif information in its appropriate three-dimensional (3D) context. This system is flexible in that users can enter sequences, keywords, structures or sequence motifs to generate visualizations. In 3MOTIF, users can search using discrete sequence motifs such as PROSITE patterns, eMOTIFs, or any other regular expression-like motif. Similarly, 3MATRIX accepts an eMATRIX position-specific scoring matrix, or will convert a multiple sequence alignment block into an eMATRIX for visualization. Each query motif is used to search the protein structure database for matches, in which the motif is then visually highlighted in three dimensions. Important properties of motifs such as sequence conservation and solvent accessible surface area are also displayed in the visualizations, using carefully chosen color shading schemes.
诸如序列比对和基序构建等计算方法，对于将相关蛋白质归类到家族中很有用，同时也有助于注释功能未知的新蛋白质。这些方法能识别蛋白质序列中保守的氨基酸，但如果没有进一步研究，就无法确定保守氨基酸的具体功能或结构作用。在这项工作中，我们展示了3MATRIX（http://3matrix.stanford.edu）和3MOTIF（http://3motif.stanford.edu），这是一个基于网络的序列基序可视化系统，能在适当的三维（3D）环境中展示序列基序信息。该系统很灵活，用户可以输入序列、关键词、结构或序列基序来生成可视化结果。在3MOTIF中，用户可以使用离散的序列基序进行搜索，如PROSITE模式、eMOTIFs或任何其他类似正则表达式的基序。同样，3MATRIX接受eMATRIX位置特异性评分矩阵，或者会将多序列比对块转换为eMATRIX以进行可视化。每个查询基序用于在蛋白质结构数据库中搜索匹配项，然后在三维空间中对基序进行视觉上的突出显示。基序的重要属性，如序列保守性和溶剂可及表面积，也会在可视化结果中使用精心选择的颜色阴影方案进行显示。
