Centre de Biologie Structurale, CNRS, INSERM, Univ. Montpellier, Montpellier 34090, France.
J Proteome Res. 2022 Jul 1;21(7):1654-1663. doi: 10.1021/acs.jproteome.1c00964. Epub 2022 Jun 1.
Cells express thousands of macromolecules, and their functioning relies on multiple networks of intermolecular interactions. These interactions can be experimentally determined at different spatial and temporal resolutions. But, physical interfaces are not often delineated directly, especially in high-throughput experiments. A large fraction of protein-protein interactions involves domain and so-called SLiMs (for Short Linear Motifs). Often, SLiMs lie in disordered regions or loops. Their small size, limited sequence conservation, and loosely folded nature prevent straightforward detection. SLiMAn (Short Linear Motif Analysis), a new web server, is provided to help thorough analysis of interactomics data. From a list of putative interactants (e.g., output from an interactomics study), SLiMs (from ELM) and SLiM-recognition domains (from Pfam) are extracted, and putative pairings are displayed. Predicted results can be filtered using motif -values, IUPred2 scores, or BioGRID interaction matches. When structural templates are available, a given SLiM and its recognition domain can be modeled using SCWRL. We illustrate here the use of SLiMAn on distinct examples, including one real-case study. We oversee wide-range applications for SLiMAn in the context of the massive analysis of protein-protein interactions. This new web server is made freely available at https://sliman.cbs.cnrs.fr.
细胞表达数千种大分子，其功能依赖于分子间相互作用的多个网络。这些相互作用可以在不同的空间和时间分辨率下进行实验确定。但是，物理界面并不总是直接划定的，特别是在高通量实验中。很大一部分蛋白质-蛋白质相互作用涉及结构域和所谓的短线性基序 (SLiMs)。通常，SLiMs 位于无序区域或环中。它们的体积小、序列保守性有限且折叠松散，这使得它们难以直接检测。SLiMAn（短线性基序分析）是一个新的网络服务器，用于帮助全面分析相互作用组学数据。从一组假定的相互作用体列表（例如，相互作用组学研究的输出）中，提取 SLiMs（来自 ELM）和 SLiM 识别结构域（来自 Pfam），并显示假定的配对。预测结果可以使用基序值、IUPred2 评分或 BioGRID 相互作用匹配进行过滤。当有结构模板时，可以使用 SCWRL 对给定的 SLiM 和其识别结构域进行建模。我们在这里通过不同的示例说明了 SLiMAn 的使用，包括一个实际案例研究。我们广泛关注 SLiMAn 在大规模蛋白质-蛋白质相互作用分析中的应用。这个新的网络服务器可以在 https://sliman.cbs.cnrs.fr 上免费获得。
