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

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CE - Biochemie

OECD FORD obor

—

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

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

Rok uplatnění

2015

Kód důvěrnosti údajů

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

Název periodika

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

—

Svazek periodika

43

Číslo periodika v rámci svazku

D1

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

7

Strana od-do

"D369"-"D375"

Kód UT WoS článku

000350210400057

EID výsledku v databázi Scopus

—