Universität Hamburg, ZBH - Center for Bioinformatics (ZBH), 20146 Hamburg, Germany.
Nucleic Acids Res. 2020 Jul 2;48(W1):W48-W53. doi: 10.1093/nar/gkaa235.
Due to the increasing amount of publicly available protein structures searching, enriching and investigating these data still poses a challenging task. The ProteinsPlus web service (https://proteins.plus) offers a broad range of tools addressing these challenges. The web interface to the tool collection focusing on protein-ligand interactions has been geared towards easy and intuitive access to a large variety of functionality for life scientists. Since our last publication, the ProteinsPlus web service has been extended by additional services as well as it has undergone substantial infrastructural improvements. A keyword search functionality was added on the start page of ProteinsPlus enabling users to work on structures without knowing their PDB code. The tool collection has been augmented by three tools: StructureProfiler validates ligands and active sites using selection criteria of well-established protein-ligand benchmark data sets, WarPP places water molecules in the ligand binding sites of a protein, and METALizer calculates, predicts and scores coordination geometries of metal ions based on surrounding complex atoms. Additionally, all tools provided by ProteinsPlus are available through a REST service enabling the automated integration in structure processing and modeling pipelines.
由于可公开获取的蛋白质结构数量不断增加，因此搜索、丰富和研究这些数据仍然是一项具有挑战性的任务。ProteinsPlus 网络服务（https://proteins.plus）提供了一系列广泛的工具，可用于应对这些挑战。该网络服务的工具集合的网络界面专注于蛋白质-配体相互作用，旨在为生命科学家提供轻松直观地访问各种功能的途径。自上一次发布以来，ProteinsPlus 网络服务增加了其他服务，并进行了大量基础设施改进。在 ProteinsPlus 的起始页上添加了关键字搜索功能，使用户能够在不知道其 PDB 代码的情况下处理结构。该工具集合通过三个工具得到了扩展：StructureProfiler 使用经过验证的蛋白质-配体基准数据集的选择标准来验证配体和活性部位，WarPP 在蛋白质的配体结合部位放置水分子，而 METALizer 则根据周围的复杂原子计算、预测和评分金属离子的配位几何形状。此外，ProteinsPlus 提供的所有工具都可通过 REST 服务获得，从而能够在结构处理和建模管道中实现自动化集成。
