Small molecule data | Drug design analysis

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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

(1)

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.

DTP / Anti-cancer Agent Mechanism Database

Provides services and resources to the academic and private-sector research communities worldwide to facilitate the discovery and development of new cancer therapeutic agents. Services available directly from DTP: (i) NCI-60 human cancer cell line screen, (ii) Molecular Target Program, (iii) Materials for research — tumor cells, chemicals, natural products and biological samples. Anti-cancer Agent Mechanism Database DTP is a set of 122 compounds with anti-cancer activity and reasonably well known mechanism of action. The list of compounds was assembled as a training set for neural network analysis of drug mechanism of action.

ChEBI / Chemical Entities of Biological Interest

A database and ontology containing information about chemical entities of biological interest. ChEBI currently includes over 46 000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery.

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.

CTRP / Cancer Therapeutics Response Portal

Links genetic, lineage, and other cellular features of cancer cell lines to small-molecule sensitivity with the goal of accelerating discovery of patient-matched cancer therapeutics. CTRP hosts an 'Informer Set' of 481 small-molecule probes and drugs that selectively target distinct nodes in cell circuitry and that collectively modulate a broad array of cell processes. The CTRP is a living resource for the biomedical research community that can be mined to develop insights into small-molecule mechanisms of action and novel therapeutic hypotheses, and to support future discovery of drugs matched to patients based on predictive biomarkers.

ChemProt

(1)

A publicly available compilation of chemical-protein-disease annotation resources that enables the study of systems pharmacology for a small molecule across multiple layers of complexity from molecular to clinical levels. In this third version, ChemProt has been updated to more than 1.7 million compounds with 7.8 million bioactivity measurements for 19,504 proteins. Within ChemProt, it is possible to navigate the chemogenomics space and to link chemically induced target perturbations to diseases and other biological outcomes. Such tools might be of interest for drug discovery, drug safety and also chemical risk assessment. ChemProt 3.0 supports predicting bioactivities on targets and off-targets for new compounds and can assist in the associations to phenotypes and side effects relationships.

NPC / NCGC Pharmaceutical Collection

A comprehensive, publically-accessible collection of approved and investigational drugs for high-throughput screening. NPC provides a valuable resource for both validating new models of disease and better understanding the molecular basis of disease pathology and intervention. It has already generated several useful probes for studying a diverse cross section of biology, including novel targets and pathways. NCGC provides access to its set of approved drugs and bioactives through the Therapeutics for Rare and Neglected Diseases (TRND) program and as part of the compound collection for the Tox21 initiative, a collaborative effort for toxicity screening among several government agencies.

KEGG DRUG

Contains a comprehensive collection of approved drugs in Japan, USA and Europe unified based on chemical structures and/or chemical components. KEGG DRUG is a database which contains information about molecular networks, such as targets, metabolizing enzymes and drug–drug interactions. All the marketed drugs in Japan, the prescription drugs but also the over-the-counter (OTC) drugs, are represented in the database, including crude drugs and Traditional Chinese Medicine (TCM) drugs.

NutriChem

Allows to explore the medicinal value of diet and elucidate the synergistic effects of natural bioactive compounds on disease phenotypes. NutriChem is a database that contains food-compound pairs between some plant-based foods and phytochemicals, as well as the food-disease associations between some plant-based foods and diseases. It was generated by text mining of 21 million MEDLINE abstracts. The incorporation of confidence scores based on the availability of support from literature or patient records may serve as future update of NutriChem.

mVOC / Microbial volatile organic compounds

Summarizes the volatilomes of bacteria and fungi. mVOC was constructed thanks to an automatic text mining procedure before being manually curated by experts. It provides a web browser that allows users to query for mass spectra peaks or for emitter and receiver of specific microbial volatile organic compounds (mVOCs). This database is searchable by compounds name, PubChem-ID, chemical formula or properties.

SMPDB / Small Molecule Pathway DataBase

An interactive, visual database containing more than 618 small molecule pathways found in humans. More than 70% of these pathways (>433) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways.

HAGR / Human Ageing Genomic Resources

Provides several online databases and tools relevant to the biology of ageing. HAGR is a web portal that hosts high-quality curated gene-centric information relevant to human ageing. All data sets are linked to each other, and each gene entry contains direct links to all other relevant entries in HAGR’s datasets. The database aims to organize the increasing amount of these information and make them accessible to the research community.

SuperDrug

Offers information of pharmaceutical ingredients. SuperDRUG provides annotated drugs with regulatory details, chemical structures (2D and 3D), dosage, biological targets, physicochemical properties, external identifiers, side-effects and pharmacokinetic data. It enables a comparison of 2D- and 3D-similarity between drugs of different indication classes elucidating structural reasons for adverse effects that might be neglected by exclusive consideration of their 2D-resemblence.

ChemDB

Provides access to about 5M commercially available small molecules. ChemDB is a chemical database that contains data coming from the electronic catalogs of over 150 chemical vendors as well as a limited number of publicly available datasets. The database includes search tools in support of systems biology and drug discovery projects. Data can be searched by structural similarity, includes several, names and annotations and users can also search virtual chemical space.

PubChem Compound

Provides unique chemical structures that come from the Substance database and more than 60 million of Compound IDs (CIDs). PubChem Compound aggregates substance records from different data sources about the same molecule through a common ‘compound’ record. It provides features that allow users to see how their structures would be handled during the standardization process when they submit a structure.

PubChem Substance

Stores depositor-contributed information of chemical structures. PubChem Substance provides more than 157 million of Substance IDs (SIDs). It can contain information such as biological functions of glucose, or characteristics of a research grade sample of glucose. This tool stores different descriptions about the same molecule as separate records that are independent of each other. It allows users to submit descriptions following a standardization process.

SCRIPDB

A chemical structure database designed to make this metadata accessible. SCRIPDB provides the full original patent text, reactions and relationships described within any individual patent, in addition to the molecular files common to structural databases. SCRIPDB may be searched by exact chemical structure, substructure or molecular similarity and the results may be restricted to patents describing synthetic routes.

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.

SureChEMBL

A publicly available large-scale resource containing compounds extracted from the full text, images and attachments of patent documents. The data are extracted from the patent literature according to an automated text and image-mining pipeline on a daily basis. SureChEMBL provides access to a previously unavailable, open and timely set of annotated compound-patent associations, complemented with sophisticated combined structure and keyword-based search capabilities against the compound repository and patent document corpus; given the wealth of knowledge hidden in patent documents, analysis of SureChEMBL data has immediate applications in drug discovery, medicinal chemistry and other commercial areas of chemical science. The SureChEMBL database contains more than 17 million distinct compounds extracted from more than 14 million patent documents, spanning a time range from 1970 to present.

Small molecule databases | Chemical informatics data analysis