Pons Jean-Luc, Labesse Gilles
A.B.C.I.S., CNRS UMR5048-Universités Montpellier 1 & Montpellier II and INSERM U554, 29, Rue de Navacelles, 34090 Montpellier Cedex, France.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W485-91. doi: 10.1093/nar/gkp368. Epub 2009 May 13.
@TOME 2.0 is new web pipeline dedicated to protein structure modeling and small ligand docking based on comparative analyses. @TOME 2.0 allows fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation. These tasks are routinely used in sequence analyses for structure prediction. In our pipeline the necessary software is efficiently interconnected in an original manner to accelerate all the processes. Furthermore, we have also connected comparative docking of small ligands that is performed using protein-protein superposition. The input is a simple protein sequence in one-letter code with no comment. The resulting 3D model, protein-ligand complexes and structural alignments can be visualized through dedicated Web interfaces or can be downloaded for further studies. These original features will aid in the functional annotation of proteins and the selection of templates for molecular modeling and virtual screening. Several examples are described to highlight some of the new functionalities provided by this pipeline. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/AT2/
@TOME 2.0是一个全新的网络流程，致力于基于比较分析进行蛋白质结构建模和小分子配体对接。@TOME 2.0支持折叠识别、模板选择、结构比对编辑、结构比较、三维模型构建与评估。这些任务在用于结构预测的序列分析中经常使用。在我们的流程中，必要的软件以一种独特的方式高效互连，以加速所有流程。此外，我们还连接了使用蛋白质-蛋白质叠合进行的小分子配体比较对接。输入是一个无注释的单字母代码简单蛋白质序列。生成的三维模型、蛋白质-配体复合物和结构比对可通过专用网络界面进行可视化，也可下载以供进一步研究。这些独特功能将有助于蛋白质的功能注释以及分子建模和虚拟筛选模板的选择。文中描述了几个示例，以突出此流程提供的一些新功能。该服务器及其文档可在http://abcis.cbs.cnrs.fr/AT2/免费获取。
