ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
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DOI：
10.1093/nar/gku1118
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发表时间：
2015-01-28
影响因子：
14.9
通讯作者：
Koca, Jaroslav
中科院分区：
文献类型：
--
作者：
Sehnal, David;Varekova, Radka Svobodova;Koca, Jaroslav
随着生物大分子结构中严重错误的发现，结构验证已成为研究的重点，特别是配体和非标准残基。ValidatorDB（可在http://ncbr.muni.cz/ValidatorDB免费获得）在这个方向上迈出了新的一步，它以数据库的形式提供了来自蛋白质数据库（所有具有7个或更多重原子的分子）的所有配体和非标准残基的验证结果。来自wwPDB化学成分字典的模型分子在验证过程中被用作参考。ValidatorDB涵盖了注释验证的主要方面，另外还介绍了几个有用的验证分析。最重要的是手性错误的分类，允许用户区分严重的问题和轻微的不一致。其他这样的分析能够报告，例如，完全错误的配体，替代构象或与模型分子完全一致。所有结果被系统地分类，并进行统计评价。除了每个分子的详细验证报告之外，ValidatorDB还为整个PDB、共享相同注释（三字母代码）或相同PDB条目的分子集以及用户定义的注释或PDB条目选择提供验证结果摘要。
Following the discovery of serious errors in the structure of biomacromolecules, structure validation has become a key topic of research, especially for ligands and non-standard residues. ValidatorDB (freely available at http://ncbr.muni.cz/ValidatorDB) offers a new step in this direction, in the form of a database of validation results for all ligands and non-standard residues from the Protein Data Bank (all molecules with seven or more heavy atoms). Model molecules from the wwPDB Chemical Component Dictionary are used as reference during validation. ValidatorDB covers the main aspects of validation of annotation, and additionally introduces several useful validation analyses. The most significant is the classification of chirality errors, allowing the user to distinguish between serious issues and minor inconsistencies. Other such analyses are able to report, for example, completely erroneous ligands, alternate conformations or complete identity with the model molecules. All results are systematically classified into categories, and statistical evaluations are performed. In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries.