Barcelona Supercomputing Center (BSC), Barcelona, Spain.
Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Utrecht, The Netherlands.
Methods Mol Biol. 2020;2112:131-144. doi: 10.1007/978-1-0716-0270-6_10.
Structural characterization of protein-protein interactions can provide essential details to understand biological functions at the molecular level and to facilitate their manipulation for biotechnological and biomedical purposes. Unfortunately, the 3D structure is available for only a small fraction of all possible protein-protein interactions, due to the technical limitations of high-resolution structural determination methods. In this context, low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be combined with computational docking to provide structural models of protein-protein interactions at large scale. In this chapter, we describe the pyDockSAXS web server ( https://life.bsc.es/pid/pydocksaxs ), which uses pyDock docking and scoring to provide structural models that optimally satisfy the input SAXS data. This server, which is freely available to the scientific community, provides an automatic pipeline to model the structure of a protein-protein complex from SAXS data.
蛋白质-蛋白质相互作用的结构特征可以提供重要的细节，帮助我们在分子水平上理解生物功能，并促进对其进行生物技术和生物医学方面的操作。不幸的是，由于高分辨率结构测定方法的技术限制，只有一小部分可能的蛋白质-蛋白质相互作用具有 3D 结构。在这种情况下，低分辨率结构技术，如小角 X 射线散射（SAXS），可以与计算对接相结合，以提供大规模蛋白质-蛋白质相互作用的结构模型。在本章中，我们描述了 pyDockSAXS 网络服务器（https://life.bsc.es/pid/pydocksaxs），该服务器使用 pyDock 对接和评分来提供最佳满足输入 SAXS 数据的结构模型。该服务器免费向科学界提供，它提供了一个从 SAXS 数据构建蛋白质-蛋白质复合物结构的自动流水线。
