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PubChem
Contains chemical structures and biological properties of molecules including small molecules and siRNA reagents. PubChem consists of three interconnected databases: Substance, BioAssay and Compound. The database also provides a suite of web-based bioactivity analysis tools allowing to download and search individual test results, compare biological activity data from multiple screenings, examine target selectivity or explore structure–activity relationships for compounds of interest.
ChEMBL
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A well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services, which exposes significantly more data from the underlying database and introduces new functionality.
KEGG
An integrated database resource consisting of 16 main databases, which are categorized into systems, genomic, chemical and health information. The PATHWAY, BRITE and MODULE databases in the systems information category contain KEGG pathway maps, BRITE hierarchy and table files and KEGG modules, respectively, as representations of high-level functions. They are all manually created based on published literature. The genomic information category contains the GENOME and GENES databases for collections of organisms with complete genomes and their gene catalogs, which are mostly taken from RefSeq and GenBank databases. The COMPOUND, GLYCAN, REACTION, RPAIR, RCLASS and ENZYME databases in the chemical information category contain chemical substances and reactions and are collectively called KEGG LIGAND for historical reasons. The health information category consists of the DISEASE, DRUG, DGROUP and ENVIRON databases for disease and drug information.
DrugBank
Gathers detailed drug, drug-target, drug action and drug interaction information about drugs. DrugBank is a web resource that contains information about FDA-approved drugs as well as experimental drugs going through the FDA approval process. The database also includes pharmaco-omic data covering the influence of drugs on metabolite levels, gene expression levels and protein expression levels, as well as data on investigational drug clinical trials and drug repurposing trials, and thousands of up-to-date drug images of approved drugs.
PubChem BioAssay
Provides about 1 million bioassay records, 30,000 protein and gene targets, 3 million tested substances, 2 million unique chemical structures, and 200 million bioactivity outcomes. PubChem BioAssay was created to archive the small-molecule high-throughput screening (HTS) data from the National Institute of Health’s (NIH) Molecular Libraries Program (MLP). The platform offers a suite of service that enable users to search, collect, compare, and analyze biological test results.
Supertarget
Integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present, the updated database contains >6,000 target proteins, which are annotated with >330,000 relations to 196,000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range.
ChemBank
A public, Web-based informatics environment. ChemBank stores and makes freely available data derived from small molecules and small-molecule screens and has resources for relating and studying these data. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays performed at the Broad Institute screening center. Web-based analysis tools are available within ChemBank to study the relationships between small molecules, cell measurements, and cell states.
MATADOR
A resource for protein-chemical interactions. MATADOR differs from other resources such as DrugBank in its inclusion of as many direct and indirect interactions as we could find. In contrast, DrugBank usually contains only the main mode of interaction. The manually annotated list of direct (binding) and indirect interactions between proteins and chemicals was assembled by automated text-mining followed by manual curation. Each interaction contains links to PubMed abstracts or OMIM entries that were used to deduce the interaction.
BARD / BioAssay Research Database
A public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions.
T3DB / Toxin-Toxin-Target DataBase
A resource that was specifically designed to capture information about the toxic exposome. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches.
CSCTT / Cancer Stem Cells Therapeutic Target Database
Provides users with biological tools and the hyperlinks to various biological databases, including UniProt, Protein Data Bank (PDB), KEGG, and PubChem. The CSCTT is a database that consists of two major types of data: (i) therapeutic targets for cancer stem cells (CSCs) and (ii) therapeutic methods for CSCs. It provides users with a brief summary of protein targets and available therapeutic methods used for CSCs with documented evidence.
MPD3 / Medicinal Plants Database for Drug Designing
Merges activities of phytochemicals from medicinal plants, their targets and literature references. MPD3 contains information about more than 5000 phytochemicals from around 1000 medicinal plants with 80 different activities, more than 900 literature references and 200 plus targets. It gives information about medicinal plants regarding classification, genus, phytochemicals, their activities, targets, literature references and offers freely ready-to-dock library to find out therapeutic capability of medicinal plants against different targets.
DIP / Drug Information Portal
Facilitates the user information retrieval using several health terminologies. DIP has created specific functionalities related to drug and used specific drugs terminologies and classifications: the ATC classification, the CAS numbers, the French codes CIS, and CIP, as well as trade names and the International Nonproprietary Names of the drugs. It gives access to information concerning more than 70,600 drugs. Search can be made with the generic name or the trade name.
TBDRUGS / Database of Drugs for Tuberculosis
Provides pharmacological, clinical, and molecular data on anti-tuberculosis drugs. TBDRUGS includes a brief description of the chemical characteristics and pharmacological properties of each drug, its route of administration, dosage (for adult as well as children in the case of approved drugs), adverse effects, mechanism of action, effect on bacteria (bactericidal/ bacteriostatic), properties, stage of development (for those in pipeline), and target details.
CREST / Chemical attributes, Regulatory approaches and Experimental STudies from a mixture toxicology perspective
Gathers information about experimental mixture studies. CREST is a public repository organized through three main categories: literature, datasets and chemicals. Searches can be made by studies or by chemicals using their name or their standard international chemical identifiers (Std InChIs). The database gives access to external links towards the corresponding literature or to content that can be exported in tab-separated text format. The database is part of the MixTox TRI (towards regulatory implementation) project.
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