Gille Christoph
Institute of Biochemistry Charité, Medical Faculty of the Humboldt University, 10117 Berlin, Monbijoustrasse 2, Germany.
Protein Sci. 2006 Jan;15(1):208-10. doi: 10.1110/ps.051882006. Epub 2005 Dec 1.
Visualization of residue positions in protein alignments and mapping onto suitable structural models is an important first step in the interpretation of mutations or polymorphisms in terms of protein function, interaction, and thermodynamic stability. Selecting and highlighting large numbers of residue positions in a protein structure can be time-consuming and tedious with currently available software. Previously, a series of tasks and analyses had to be performed one-by-one to map mutations onto 3D protein structures; STRAP-NT is an extension of STRAP that automates these tasks so that users can quickly and conveniently map mutations onto 3D protein structures. When the structure of the protein of interest is not yet available, a related protein can frequently be found in the structure databases. In this case the alignment of both proteins becomes the crucial part of the analysis. Therefore we embedded these program modules into the Java-based multiple sequence alignment program STRAP-NT. STRAP-NT can simultaneously map an arbitrary number of mutations denoted using either the nucleotide or amino acid sequence. When the designations of the mutations refer to genomic sites, STRAP-NT translates them into the corresponding amino acid positions, taking intron-exon boundaries into account. STRAP-NT tightly integrates a number of current protein structure viewers (currently PYMOL, RASMOL, JMOL, and VMD) with which mutations and polymorphisms can be directly displayed on the 3D protein structure model. STRAP-NT is available at the PDB site and at http://www.charite.de/bioinf/strap/ or http://strapjava.de.
在蛋白质比对中可视化残基位置并映射到合适的结构模型上，是从蛋白质功能、相互作用和热力学稳定性方面解释突变或多态性的重要第一步。使用现有的软件在蛋白质结构中选择并突出显示大量残基位置既耗时又繁琐。以前，必须逐一执行一系列任务和分析才能将突变映射到三维蛋白质结构上；STRAP-NT是STRAP的扩展版本，它能自动执行这些任务，以便用户可以快速方便地将突变映射到三维蛋白质结构上。当目标蛋白质的结构尚不可用时，通常可以在结构数据库中找到相关蛋白质。在这种情况下，两种蛋白质的比对就成为分析的关键部分。因此，我们将这些程序模块嵌入到基于Java的多序列比对程序STRAP-NT中。STRAP-NT可以同时映射任意数量的使用核苷酸或氨基酸序列表示的突变。当突变的标识指的是基因组位点时，STRAP-NT会将它们转换为相应的氨基酸位置，并考虑内含子-外显子边界。STRAP-NT紧密集成了许多当前的蛋白质结构查看器（目前有PYMOL、RASMOL、JMOL和VMD），通过这些查看器可以直接在三维蛋白质结构模型上显示突变和多态性。STRAP-NT可在PDB网站以及http://www.charite.de/bioinf/strap/或http://strapjava.de获取。
