Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England.
Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic.
Acta Crystallogr D Struct Biol. 2018 Mar 1;74(Pt 3):237-244. doi: 10.1107/S2059798318003303. Epub 2018 Mar 2.
Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrends database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.
认识到评估蛋白质数据库（PDB）中生物分子结构质量的重要性，全球蛋白质数据库（wwPDB）合作伙伴成立了验证工作组，以就用于验证 X 射线晶体学、核磁共振波谱学和三维电子晶体学确定的结构的方法和标准获取建议。由此产生的 wwPDB 验证管道是 wwPDB OneDep 沉积、生物注释和验证系统的一个组成部分。wwPDB 验证服务网络服务器（https://validate.wwpdb.org）可用于在沉积前进行检查。在这里，展示了如何将验证指标组合在一起，生成一个总分，以便对搜索结果中的大分子结构和结构域进行排名。ValTrends 数据库为用户提供了一种方便的方法来访问和分析 PDB 中 X 射线晶体结构的验证信息和其他属性，包括研究不同结构属性和验证指标之间的趋势和相关性。
