Garcia-Boronat Maria, Diez-Rivero Carmen M, Reinherz Ellis L, Reche Pedro A
Immunomedicine Group, Department of Microbiology I, Division of Immunology, Facultad de Medicina, Universidad Complutense de Madrid, Ave Complutense s/n, Madrid 28040, Spain.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W35-41. doi: 10.1093/nar/gkn211. Epub 2008 Apr 27.
We have developed PVS (Protein Variability Server), a web-based tool that uses several variability metrics to compute the absolute site variability in multiple protein-sequence alignments (MSAs). The variability is then assigned to a user-selected reference sequence consisting of either the first sequence in the alignment or a consensus sequence. Subsequently, PVS performs tasks that are relevant for structure-function studies, such as plotting and visualizing the variability in a relevant 3D-structure. Neatly, PVS also implements some other tasks that are thought to facilitate the design of epitope discovery-driven vaccines against pathogens where sequence variability largely contributes to immune evasion. Thus, PVS can return the conserved fragments in the MSA-as defined by a user-provided variability threshold-and locate them in a relevant 3D-structure. Furthermore, PVS can return a variability-masked sequence, which can be directly submitted to the RANKPEP server for the prediction of conserved T-cell epitopes. PVS is freely available at: http://imed.med.ucm.es/PVS/.
我们开发了PVS（蛋白质变异性服务器），这是一种基于网络的工具，它使用多种变异性指标来计算多个蛋白质序列比对（MSA）中的绝对位点变异性。然后将变异性分配给用户选择的参考序列，该参考序列可以是比对中的第一个序列或共有序列。随后，PVS执行与结构-功能研究相关的任务，例如绘制和可视化相关三维结构中的变异性。巧妙的是，PVS还实现了一些其他任务，这些任务被认为有助于设计针对病原体的表位发现驱动型疫苗，其中序列变异性在很大程度上导致了免疫逃逸。因此，PVS可以返回MSA中由用户提供的变异性阈值定义的保守片段，并将它们定位在相关的三维结构中。此外，PVS可以返回一个变异性掩码序列，该序列可以直接提交给RANKPEP服务器以预测保守的T细胞表位。PVS可在以下网址免费获取：http://imed.med.ucm.es/PVS/ 。
