ProtCID

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.

蛋白质与其他分子相互作用的结构信息储量丰富，针对部分蛋白质及蛋白质家族，已有数百个可用的三维结构。未接受过结构生物信息学训练的科研人员往往难以全面获取这类信息。此前我们开发了蛋白质共同界面数据库（Protein Common Interface Database，ProtCID），该库通过提供全长蛋白质链的界面簇来辅助识别生物组装体。由于蛋白质由作为模块化功能单元的结构域构成，我们将ProtCID的分析范围拓展至单个结构域层面。这一拓展大幅增加了ProtCID中大型蛋白质-蛋白质簇的数量，支持针对诸多系统的生物组装体结构生成研究假说。针对结构域家族的分析让我们得以将ProtCID的覆盖范围进一步拓展至结构域与肽、核酸以及配体的相互作用。ProtCID为每个簇提供完整的注释信息与原子坐标集。