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

J 2015

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

SEHNAL, David; Radka SVOBODOVÁ VAŘEKOVÁ; Lukáš PRAVDA; Crina-Maria IONESCU; Stanislav GEIDL et al.

Základní údaje

Originální název

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

Autoři

SEHNAL, David; Radka SVOBODOVÁ VAŘEKOVÁ; Lukáš PRAVDA; Crina-Maria IONESCU; Stanislav GEIDL; Vladimír HORSKÝ; Deepti JAISWAL; Michaela WIMMEROVÁ a Jaroslav KOČA

Vydání

Nucleic Acids Research, United Kingdom, Oxford University Press, 2015, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 9.202

Kód RIV

RIV/00216224:14310/15:00082165

Organizační jednotka

Přírodovědecká fakulta

DOI

https://doi.org/10.1093/nar/gku1118

UT WoS

000350210400057

EID Scopus

2-s2.0-84941074422

Klíčová slova anglicky

chemical analysis; chemical structure; chirality; computer program; data analysis; data base; molecular model; process development; Protein Data Bank; systematic error; validation process; ValidatorDB

Štítky

AKR, OA, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 29. 3. 2016 11:26, Olga Křížová

Anotace

V originále

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

EE2.3.20.0042, projekt VaV

Název: Internacionalizace programu Strukturní biologie s důrazem na rozvoj nových směrů výzkumu

EE2.3.30.0009, projekt VaV

Název: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci

LH13055, projekt VaV

Název: Multidisciplinární přístup k návrhu léčiv - Inhibice proteinů s návazností na cukry (Akronym: MADICA)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Multidisciplinární přístup k návrhu léčiv - Inhibice proteinů s návazností na sacharidy

MUNI/A/0855/2013, interní kód MU

Název: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace III. (Akronym: FI MAV III.)

Investor: Masarykova univerzita, Rozsáhlé výpočetní systémy: modely, aplikace a verifikace III., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

MUNI/A/1159/2014, interní kód MU

Název: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace IV.

Investor: Masarykova univerzita, Rozsáhlé výpočetní systémy: modely, aplikace a verifikace IV., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

286154, interní kód MU

Název: SYLICA - Synergies of Life and Material Sciences to Create a New Future (Akronym: SYLICA)

Investor: Evropská unie, SYLICA - Synergies of Life and Material Sciences to Create a New Future, Kapacity

Přiložené soubory

1206145_ValidatorDB_databse_of_up-to-date.pdf

Požádat o autorskou verzi souboru

Citovat

SEHNAL, David; Radka SVOBODOVÁ VAŘEKOVÁ; Lukáš PRAVDA; Crina-Maria IONESCU; Stanislav GEIDL; Vladimír HORSKÝ; Deepti JAISWAL; Michaela WIMMEROVÁ a Jaroslav KOČA. ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Research. United Kingdom: Oxford University Press, 2015, roč. 43, D1, s. "D369"-"D375", 7 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gku1118.

@article{1206145,
   author = {Sehnal, David and Svobodová Vařeková, Radka and Pravda, Lukáš and Ionescu, CrinaandMaria and Geidl, Stanislav and Horský, Vladimír and Jaiswal, Deepti and Wimmerová, Michaela and Koča, Jaroslav},
   article_location = {United Kingdom},
   article_number = {D1},
   doi = {https://doi.org/10.1093/nar/gku1118},
   keywords = {chemical analysis; chemical structure; chirality; computer program; data analysis; data base; molecular model; process development; Protein Data Bank; systematic error; validation process; ValidatorDB},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank},
   url = {http://nar.oxfordjournals.org/content/43/D1/D369.full.pdf+html},
   volume = {43},
   year = {2015}
}

TY  - JOUR
ID  - 1206145
AU  - Sehnal, David - Svobodová Vařeková, Radka - Pravda, Lukáš - Ionescu, Crina-Maria - Geidl, Stanislav - Horský, Vladimír - Jaiswal, Deepti - Wimmerová, Michaela - Koča, Jaroslav
PY  - 2015
TI  - ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
JF  - Nucleic Acids Research
VL  - 43
IS  - D1
SP  - "D369"-"D375"
EP  - "D369"-"D375"
PB  - Oxford University Press
SN  - 03051048
KW  - chemical analysis
KW  - chemical structure
KW  - chirality
KW  - computer program
KW  - data analysis
KW  - data base
KW  - molecular model
KW  - process development
KW  - Protein Data Bank
KW  - systematic error
KW  - validation process
KW  - ValidatorDB
UR  - http://nar.oxfordjournals.org/content/43/D1/D369.full.pdf+html
L2  - http://nar.oxfordjournals.org/content/43/D1/D369.full.pdf+html
N2  - 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.
ER  -

SEHNAL, David; Radka SVOBODOVÁ VAŘEKOVÁ; Lukáš PRAVDA; Crina-Maria IONESCU; Stanislav GEIDL; Vladimír HORSKÝ; Deepti JAISWAL; Michaela WIMMEROVÁ a Jaroslav KOČA. ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. \textit{Nucleic Acids Research}. United Kingdom: Oxford University Press, 2015, roč.~43, D1, s.~''D369''-''D375'', 7 s. ISSN~0305-1048. Dostupné z: https://doi.org/10.1093/nar/gku1118.

Přehled o publikaci