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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F15%3A00082165" target="_blank" >RIV/00216224:14310/15:00082165 - isvavai.cz</a>

Result on the web

<a href="http://nar.oxfordjournals.org/content/43/D1/D369.full.pdf+html" target="_blank" >http://nar.oxfordjournals.org/content/43/D1/D369.full.pdf+html</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gku1118" target="_blank" >10.1093/nar/gku1118</a>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CE - Biochemistry

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Publication year

2015

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

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Volume of the periodical

43

Issue of the periodical within the volume

D1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

7

Pages from-to

"D369"-"D375"

UT code for WoS article

000350210400057

EID of the result in the Scopus database

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