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Protocols

CCD specifications

Information


Unique identifier OMICS_07428
Name CCD
Alternative name Chemical Component Dictionary
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline John D. Westbrook

Publication for Chemical Component Dictionary

CCD citations

 (7)
call_split

Validation of Structures in the Protein Data Bank

2017
PMCID: 5718880
PMID: 29174494
DOI: 10.1016/j.str.2017.10.009
call_split See protocol

[…] h in the compound is compared against the distribution of values found in comparable fragments in the CSD, and outliers are highlighted. Chirality problems are diagnosed by checking against the wwPDB Chemical Component Dictionary definitions ().The fit of the atomic model to experimental data (currently only available for X-ray crystal structures) is analyzed by the procedure developed for the Upp […]

call_split

Glycoblocks: a schematic three dimensional representation for glycans and their interactions

2016
Acta Crystallogr D Struct Biol
PMCID: 5297921
PMID: 28177314
DOI: 10.1107/S2059798316013553
call_split See protocol

[…] rmed with the CCP4 program Privateer (Agirre, Iglesias-Fernández et al., 2015) identified which sugars were present in the deposited structures, generating a list of three-letter codes from the PDB’s chemical component dictionary. Privateer’s most recent version (MKIII) introduced a Python scripting interface for seamless integration into other programs and pipelines (e.g. CCP4mg and CCP4i2, which […]

library_books

Smiles2Monomers: a link between chemical and biological structures for polymers

2015
J Cheminform
PMCID: 4693424
PMID: 26715946
DOI: 10.1186/s13321-015-0111-5

[…] As mentioned in Materials part, we use two independent sets, the Norine database and the Chemical Component Dictionary (CCD) to validate the s2m tool. We run s2m on polymers of each set, using their respective monomer databases and chemical reaction rules designed by ourselves. The aim wa […]

library_books

Automatic generation of bioinformatics tools for predicting protein–ligand binding sites

2015
Bioinformatics
PMCID: 4803387
PMID: 26545824
DOI: 10.1093/bioinformatics/btv593

[…] atabase schema of PLBSP in RDF for analyzed in-house data. This database was constructed from all ligand-binding protein structures in the PDB. We used a public RDF dataset and ontology from PDB, PDB Chemical Component Dictionary (CCD) and UniProt with in-house data for the annotation. PDB sequences were mapped to UniProt to link multiple PDB sequences to a sequence, to obtain full protein sequenc […]

library_books

Conformational readout of RNA by small ligands

2013
RNA Biol
PMCID: 4111737
PMID: 23618839
DOI: 10.4161/rna.24682

[…] romatic carbon atoms of the RNA and aromatic carbon atoms of the ligand not involved in hydrogen bonds that were < 3.9Å apart. Aromatic carbon atoms of the ligand were determined according to the PDB chemical component dictionary. […]

library_books

Minimal Functional Sites Allow a Classification of Zinc Sites in Proteins

2011
PLoS One
PMCID: 3197139
PMID: 22043316
DOI: 10.1371/journal.pone.0026325

[…] TZ, HE5, HES, ZEM, ZH3, ZN, ZN2, ZN3, ZNH, ZNO, and ZO3. At the time of the download (January 2011), these were all the non-standard PDB residues containing at least one zinc atom as described in the Chemical Component Dictionary (http://www.wwpdb.org/ccd.html). Zinc sites in each structure were identified by taking all the zinc atoms in the structure, and considering zinc atoms at a distance of l […]


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CCD institution(s)
RCSB PDB, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA; Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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