ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.

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

SUBMITTER: Sehnal D 

PROVIDER: S-EPMC4383933 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature