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Protocols

ChemDB specifications

Information


Unique identifier OMICS_02738
Name ChemDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Pierre Baldi

Publications for ChemDB

ChemDB citations

 (8)
library_books

T Time: A data repository of T cell and calcium release activated calcium channel activation imagery

2017
BMC Res Notes
PMCID: 5557281
PMID: 28807036
DOI: 10.1186/s13104-017-2739-x

[…] f independent evaluation the effectiveness of different practices.Additionally, there has been wide spread adoption of large open access databases in several other scientific fields []. These include ChemDB, a public database containing small molecules and related chemoinformatics resources [], Uniprot, a database of protein sequence and functional information, which was created in collaboration w […]

library_books

Evolution of Chemosensory Gene Families in Arthropods: Insight from the First Inclusive Comparative Transcriptome Analysis across Spider Appendages

2016
Genome Biol Evol
PMCID: 5381604
PMID: 28028122
DOI: 10.1093/gbe/evw296

[…] the protein models from A. geniculata, L. hesperus, L. reclusa, M. martensii, M. occidentalis and P. tepidariorum), we approximated the functional annotation using InterProScan version 5.4.47 ().The chemDB database contains the amino acid sequences and the functional information of all well-annotated members of the Or, Gr Ir, Csp, Obp, Npc2 and Snmp gene families from a representative set of inse […]

library_books

bioassayR: Cross Target Analysis of Small Molecule Bioactivity

2016
J Chem Inf Model
PMCID: 5330305
PMID: 27367556
DOI: 10.1021/acs.jcim.6b00109

[…] decade against a wide array of distinct protein target families. The resulting high throughout screening (HTS) data are available in community driven databases such as PubChem Bioassay, ChEMBL, ZINC, ChemDB, and many others (list in Table S1 of the Supporting Information).− As demonstrated by many data mining efforts, these bioactivity resources provide an opportunity for studying the selectivity […]

library_books

An Infrastructure to Mine Molecular Descriptors for Ligand Selection on Virtual Screening

2014
Biomed Res Int
PMCID: 4000951
PMID: 24812613
DOI: 10.1155/2014/325959

[…] consider this tool in our work.Besides the molecular docking tool, the VS strategy involves the use of ligand databases. As reviewed in [] the most important public compounds database is ChemBank [], ChemDB [], NCI Database [], PubChem [], and ZINC []. In this work we choose to use the ZINC database since it is a free database of commercially available compounds that contains over 22 million purch […]

library_books

Scalable prediction of compound protein interactions using minwise hashing

2013
BMC Syst Biol
PMCID: 4029277
PMID: 24564870
DOI: 10.1186/1752-0509-7-S6-S3

[…] fingerprint representation has a long history in chemoinformatics, and many 1D, 2D or 3D descriptors for molecules have been proposed [] and adopted in many molecular databases such as PubChem [] and ChemDB []. The fingerprints can be used for exploring the chemical space based on their Euclidian distance or Tanimoto coefficients, and can also be used as inputs of various machine learning classifi […]

call_split

Docking studies and network analyses reveal capacity of compounds from Kandelia rheedii to strengthen cellular immunity by interacting with host proteins during tuberculosis infection

2012
Bioinformation
PMCID: 3524883
PMID: 23275699
DOI: 10.6026/97320630081012
call_split See protocol

[…] The 3D ligand structure was downloaded from online database ChemDB (http://cdb.ics.uci.edu/) and was subsequently docked to protein 3D structure of the macromolecule. Target molecule sequences were collected from NCBI Proteins database. The macromolecule 3D st […]


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ChemDB institution(s)
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, USA
ChemDB funding source(s)
Supported by an NIH Biomedical Informatics Training grant (LM-07443-01) and NSF grants EIA-0321390 and 0513376.

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