ValidatorDB
Names
More detailed information about this field from each metasource.
ValidatorDB
metasource: Fairsharing.org
version: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
validatordb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Names
More detailed information about this field from each metasource.
ValidatorDB
metasource: Fairsharing.orgversion: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
validatordb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
Names
More detailed information about this field from each metasource.
ValidatorDB
metasource: Fairsharing.orgversion: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
validatordb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
ValidatorDB is a collection of validation results for the entire Protein Data Bank. Annotation (3-letter code) of HET residues larger than 6 heavy atoms is inspected, i.e. if the residue has the same topology and stereochemistry as the model ligand or residue stored in the wwCCD. Validation reports for the entire database can be inspected as well as for the arbitrary set of PDB entries or PDB annotations (3-letter residue code). Results are available in graphical form via Web UI and can be downloaded in the form of CSV files for further inspection.
Description
More detailed information about this field from each metasource.
ValidatorDB is a collection of validation results for the entire Protein Data Bank. Annotation (3-letter code) of HET residues larger than 6 heavy atoms is inspected, i.e. if the residue has the same topology and stereochemistry as the model ligand or residue stored in the wwCCD. Validation reports for the entire database can be inspected as well as for the arbitrary set of PDB entries or PDB annotations (3-letter residue code). Results are available in graphical form via Web UI and can be downloaded in the form of CSV files for further inspection.
metasource: Fairsharing.orgversion: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Precomputed validation results for ligands and residues in the PDB
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Database of validation results for ligands and non-standard residues in the Protein Data Bank.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
Webpage:
http://webchem.ncbr.muni.cz/Platform/ValidatorDBWebpage
More detailed information about this field from each metasource.
http://webchem.ncbr.muni.cz/Platform/ValidatorDB
metasource: Fairsharing.orgversion: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
http://ncbr.muni.cz/ValidatorDB
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: ValidatorDB Terms of UseLicence name
More detailed information about this field from each metasource.
ValidatorDB Terms of Use
metasource: Fairsharing.orgversion: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Licence URL
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http://webchem.ncbr.muni.cz/Platform/Home/TermsOfUse
metasource: Fairsharing.orgversion: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
PMID: 25392418
metasource: Fairsharing.org
version: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gku1118
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Publications
More detailed information about this field from each metasource.
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
PMID: 25392418
metasource: Fairsharing.org
version: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gku1118
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
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ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
PubMed citations: 14.
14 articles citing: ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. PMID:33322545
High-performance macromolecular data delivery and visualization for the web. PMID:33263322
Three-Dimensional Structures of Carbohydrates and Where to Find Them. PMID:33081008
A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform. PMID:31390767
ValTrendsDB: bringing Protein Data Bank validation information closer to the user. PMID:31263870
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
PDBsum: Structural summaries of PDB entries. PMID:28875543
Tools for ligand validation in Coot. PMID:28291755
The Eighth Central European Conference "Chemistry towards Biology": Snapshot. PMID:27763518
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. PMID:27050687
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. PMID:26013810
Three-dimensional structures in the design of therapeutics targeting parasitic protozoa: reflections on the past, present and future. PMID:25945701
Models of protein-ligand crystal structures: trust, but verify. PMID:25665575
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. PMID:25593347 - http://dx.doi.org/10.1093/nar/gku1118
Tags:
Tags
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ligand
metasource: Fairsharing.org
version: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Tags
More detailed information about this field from each metasource.
ligand
metasource: Fairsharing.orgversion: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: ValidatorDB; ValidatorDB; DOI: https://doi.org/10.25504/FAIRsharing.c9psgb; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
small molecules
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
ligand protein structure small molecule structure structure structure analysis small molecule
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