Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
Nat Commun. 2020 Feb 5;11(1):711. doi: 10.1038/s41467-020-14301-4.
Structural information on the interactions of proteins with other molecules is plentiful, and for some proteins and protein families, there may be 100s of available structures. It can be very difficult for a scientist who is not trained in structural bioinformatics to access this information comprehensively. Previously, we developed the Protein Common Interface Database (ProtCID), which provided clusters of the interfaces of full-length protein chains as a means of identifying biological assemblies. Because proteins consist of domains that act as modular functional units, we have extended the analysis in ProtCID to the individual domain level. This has greatly increased the number of large protein-protein clusters in ProtCID, enabling the generation of hypotheses on the structures of biological assemblies of many systems. The analysis of domain families allows us to extend ProtCID to the interactions of domains with peptides, nucleic acids, and ligands. ProtCID provides complete annotations and coordinate sets for every cluster.
关于蛋白质与其他分子相互作用的结构信息非常丰富，对于一些蛋白质和蛋白质家族，可能有数百个可用的结构。对于没有接受过结构生物信息学培训的科学家来说，全面获取这些信息可能非常困难。此前，我们开发了蛋白质公共界面数据库（ProtCID），它提供全长蛋白质链的界面簇，作为识别生物组装的一种手段。由于蛋白质由作为模块化功能单元的结构域组成，我们已经将 ProtCID 中的分析扩展到了单个结构域级别。这极大地增加了 ProtCID 中大型蛋白质-蛋白质簇的数量，使得可以对许多系统的生物组装结构提出假设。结构域家族的分析使我们能够将 ProtCID 扩展到结构域与肽、核酸和配体的相互作用。ProtCID 为每个簇提供完整的注释和坐标集。
