ArticleNucleic acids research2015
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans.Biomolecules · 2020Article
- High-performance macromolecular data delivery and visualization for the web.Acta crystallographica. Section D, Structural biology · 2020Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- ValTrendsDB: bringing Protein Data Bank validation information closer to the user.Bioinformatics (Oxford, England) · 2019Article
- A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform.Medicines (Basel, Switzerland) · 2019Article
- Worldwide Protein Data Bank validation information: usage and trends.Acta crystallographica. Section D, Structural biology · 2018Article
- PDBsum: Structural summaries of PDB entries.Protein science : a publication of the Protein Society · 2018Article
- Tools for ligand validation in Coot.Acta crystallographica. Section D, Structural biology · 2017Article
- The Eighth Central European Conference "Chemistry towards Biology": Snapshot.Molecules (Basel, Switzerland) · 2016Article
- Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.Structure (London, England : 1993) · 2016Article
- Models of protein-ligand crystal structures: trust, but verify.Journal of computer-aided molecular design · 2015Article
- PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.Nucleic acids research · 2015Article
- Three-dimensional structures in the design of therapeutics targeting parasitic protozoa: reflections on the past, present and future.Acta crystallographica. Section F, Structural biology communications · 2015Review
- The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.Nucleic acids research · 2015Article
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9 authors.
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Abstract
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.
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