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Natural compound databases | Drug discovery

Many natural products have pharmacological or biological activities that can be of therapeutic benefit in treating diseases, and are also an important source of inspiration for development of potential novel drugs. The past few decades have…
PubChem
Dataset

PubChem

Contains chemical structures and biological properties of molecules including…

Contains chemical structures and biological properties of molecules including small molecules and siRNA reagents. PubChem consists of three interconnected databases: Substance, BioAssay and Compound.…

GNPS
Dataset

GNPS Global Natural Products Social Molecular Networking

An open-access knowledge base for community-wide organization and sharing of…

An open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS provides a community-led knowledge space in which…

TCMSP
Dataset
ChemBank
Dataset

ChemBank

A public, Web-based informatics environment. ChemBank stores and makes freely…

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…

TCM…
Dataset

TCM Database@Taiwan

Gathers information about herbs, animal products and minerals listed from…

Gathers information about herbs, animal products and minerals listed from Chinese medical texts, dictionaries, Medline and ISI Web of Knowledge. TCM Database@Taiwan contains more than 20000…

StreptomeDB
Dataset

StreptomeDB

A database of natural products isolated from Streptomyces. StreptomeDB 2.0…

A database of natural products isolated from Streptomyces. StreptomeDB 2.0 represents a major step forward: its content has been increased to over 4000 compounds and more than 2500 host organisms. In…

MedCrawler
Desktop

MedCrawler

Finds, extracts and displays medical terms from blog posts. MedCrawler is a…

Finds, extracts and displays medical terms from blog posts. MedCrawler is a data mining tool for analyzing user-generated blog posts aiming to find modern ‘traditional’ medicine or home remedies.…

Super Natural
Dataset

Super Natural

A database of natural products. Super Natural contains 325,508 natural…

A database of natural products. Super Natural contains 325,508 natural compounds (NCs), including information about the corresponding 2d structures, physicochemical properties, predicted toxicity…

Carotenoids…
Dataset

Carotenoids Database

Provides information on 1158 natural carotenoids with 692 source organisms.…

Provides information on 1158 natural carotenoids with 692 source organisms. Carotenoids Database hosts data on their structures and source organisms which were obtained from the latest available…

DisArticle
Web

DisArticle

Searches for articles only on traditional medicine in Northeast Asia, including…

Searches for articles only on traditional medicine in Northeast Asia, including traditional Chinese medicine. DisArticle is a web server in which users can search for the articles and obtain…

TBC2health
Dataset

TBC2health Tea Bioactive Compounds

A database that currently documents 1338 relationships between 497 tea…

A database that currently documents 1338 relationships between 497 tea bioactive compounds and 206 diseases (or phenotypes) manually culled from over 300 published articles. TBC2health contains…

PDTCM
Dataset

PDTCM Psoriasis Database of Traditional Chinese Medicine

Provides users a psoriasis database of traditional Chinese medicine with…

Provides users a psoriasis database of traditional Chinese medicine with systems pharmacology-based methods. PDTCM comprises eight data entities including herbal formulas, Traditional Chinese…

NANPDB
Dataset

NANPDB Northern African Natural Products Database

Gathers information about Natural products from Northern Africa. NANPDB aims to…

Gathers information about Natural products from Northern Africa. NANPDB aims to provide a library of various compounds (mainly from plants but also including from some endophytes, animals, fungi, and…

Microsource
Web

Microsource

Provides an economical and comprehensive source for first assay explorations.…

Provides an economical and comprehensive source for first assay explorations. Microsource is a system specializes in High Throughput Screening (HTS).

CEMTDD
Dataset

CEMTDD Chinese Ethnic Minority Traditional Drug

Contains about 621 herbs, 4,060 compounds, 2,163 targets and 210 diseases,…

Contains about 621 herbs, 4,060 compounds, 2,163 targets and 210 diseases, among which most of herbs can be applied into gerontology therapy including inflammation, cardiovascular disease and…

TCMID
Dataset

TCMID Traditional Chinese Medicine Integrated Database

Modernizes and standardizes Traditional Chinese Medicine (TCM). TCMID gathers…

Modernizes and standardizes Traditional Chinese Medicine (TCM). TCMID gathers data such as prescription ingredients and mass spectrometry (MS) spectra aiming to promote the TCM applications worldwide…

TarNet
Dataset

TarNet

A manually curated database and platform of traditional medicinal plants with…

A manually curated database and platform of traditional medicinal plants with natural compounds that includes potential bio-target information. We gathered information on proteins that are related to…

NPASS
Dataset

NPASS Natural Product Activity and Species Source

Provides literature-reported experimentally-determined activity values and…

Provides literature-reported experimentally-determined activity values and species sources of significantly higher number of natural products (NPs). NPASS is an online resource in which contents can…

FlavorDB
Dataset

FlavorDB

Integrates multidimensional aspects of flavor molecules. FlavorDB provides a…

Integrates multidimensional aspects of flavor molecules. FlavorDB provides a comprehensive repository of flavor molecules, flavor profiles, physicochemical properties and natural sources. By bringing…

TCM-MESH
Dataset

TCM-MESH Traditional Chinese Medicine MESH

Compiles information about Traditional Chinese Medicine (TCM) preparations. The…

Compiles information about Traditional Chinese Medicine (TCM) preparations. The database contains data about herbs, compounds, compounds gene-interactions, genes, gene interactions, diseases,…

IMPPAT
Dataset

IMPPAT Indian Medicinal Plants, Phytochemistry And Therapeutics

Gathers information about traditional Indian medicine. IMPPAT is a manually…

Gathers information about traditional Indian medicine. IMPPAT is a manually curated database from scientific literature which aims to support in silico drug discovery. It assembles over 1700 Indian…

TriForC…
Dataset

TriForC database

Covers all plant triterpene biosynthesis enzymes biochemically characterized.…

Covers all plant triterpene biosynthesis enzymes biochemically characterized. TriForC database contains about 270 enzymes from 70 different plant species that are able to catalyse over 700 reactions.…

NPCARE
Dataset

NPCARE Natural Products CARE

Contains natural products and fractional extracts for cancer regulation. NPCARE…

Contains natural products and fractional extracts for cancer regulation. NPCARE offers 6578 natural compounds and 2566 fractional extracts isolated from 1952 distinct biological species including…

TaxKB
Dataset

TaxKB Taxane Knowledge Base

Holds data on 42 parameters of 250 natural and 503 semisynthetic analogs of…

Holds data on 42 parameters of 250 natural and 503 semisynthetic analogs of taxanes. TaxKB enables the user to search data on the structure, drug-likeness, and physicochemical properties of both…

Herbalog
Dataset

Herbalog

Allows users to search about herbs. Herbalog includes more than 5110…

Allows users to search about herbs. Herbalog includes more than 5110 phytochemicals from 197 common herbs and a script that prioritizes these herbs according to their hit rates calculated through…

Np-likeness
Desktop

Np-likeness Natural product-likeness

Calculates Natural Product (NP)-likeness of a molecule, i.e. the similarity of…

Calculates Natural Product (NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. NP-likeness is a useful criterion to screen…

Traditional…
Dataset

Traditional Chinese Medicine Drugs Information System

Provides chemical compounds isolated from Chinese traditional herbs. The…

Provides chemical compounds isolated from Chinese traditional herbs. The Traditional Chinese Medicine Drugs Information System is a 3D structure database. This system enables (i) easy retrieval…

CHEM-TCM
Dataset

CHEM-TCM Chemical Database of Traditional Chinese Medicine

Contains data on known chemical constituents of 240 commonly used Chinese…

Contains data on known chemical constituents of 240 commonly used Chinese herbs. CHEM-TCM consists of four major parts: chemical identification, botanical information, predicted activity against…

SuperToxic
Dataset

SuperToxic

A collection of toxic compounds from literature and web sources. The current…

A collection of toxic compounds from literature and web sources. The current version of this database compiles about 60,000 compounds and their structures. These molecules are classified according to…

NPACT
Dataset

NPACT

A curated database of Plant derived natural compounds that exhibit…

A curated database of Plant derived natural compounds that exhibit anti-cancerous activity.

BATMAN-TCM
Web
HerDing
Web

HerDing

A search engine focused on retrieving candidate herb-related information with…

A search engine focused on retrieving candidate herb-related information with user search terms (a list of genes, a disease name, a chemical name or an herb name). HerDing integrated herb-chemical,…

EssOilDB
Dataset

EssOilDB ESSential OIL DataBase

Provides a library compiling plant essential oils. EssOilDB provides detailed…

Provides a library compiling plant essential oils. EssOilDB provides detailed information such as family information about the source plant, origin of the material and complete literature citation.…

NuBBEDB
Dataset

NuBBEDB NuBBE database

Collects classes of secondary metabolites and derivatives from the biodiversity…

Collects classes of secondary metabolites and derivatives from the biodiversity of Brazil. NuBBEDB is a database of compounds from species of the Brazilian biodiversity, especially from the two main…

TMDB
Dataset

TMDB Tea Metabolome database

A freely available electronic database containing detailed information about…

A freely available electronic database containing detailed information about small molecular metabolites found in tea including from different parts of tea plant and different tea products. It is…

Ayurveda
Dataset

Ayurveda

Provides a resource for ayurvedic phytocomponents of medicinal plants. Ayurveda…

Provides a resource for ayurvedic phytocomponents of medicinal plants. Ayurveda contains more than 50 medicinal plants, 1900 phytocomponents, and around 950 natural compounds. The components selected…

SerpentinaDB
Dataset

SerpentinaDB

Provides the whole Rauvolfia serpentina molecules facilitating prospection for…

Provides the whole Rauvolfia serpentina molecules facilitating prospection for therapeutic molecules from a medicinally important source of natural products. SerpentinaDB provides refined search…

Phytochemica
Dataset

Phytochemica

Provides comprehensive information of plant-derived molecules (PDMs) from five…

Provides comprehensive information of plant-derived molecules (PDMs) from five medicinal plants (A. belladonna, C. roseus, H. indicum, P. kurroa, P. hexandrum) as a structured and integrated library.…

SANCDB
Dataset

SANCDB South African natural compound database

A curated and fully-referenced database containing compound information for 600…

A curated and fully-referenced database containing compound information for 600 natural products extracted directly from journal articles, book chapters and theses. There is a web interface to the…

TM-MC
Dataset

TM-MC

Provides information on the constituent compounds of medicinal plant materials…

Provides information on the constituent compounds of medicinal plant materials in Northeast Asian traditional medicine. Information on the constituent compounds of these medicinal materials was…

NAPROC-13
Dataset

NAPROC-13

A database containing (13)C spectral information of over 6,000 natural…

A database containing (13)C spectral information of over 6,000 natural compounds, which allows for fast identifications of known compounds present in the crude extracts and provides insight into the…

3DMET
Dataset

3DMET 3D-structure database of natural METabolites

A database collecting three-dimensional structures of natural metabolites.…

A database collecting three-dimensional structures of natural metabolites. Three-dimensional structure is an important factor for molecular recognition. This recognition is always performed in the…

AfroDb
Dataset

AfroDb

Represents the largest “drug-like” and diverse collection of 3D structures…

Represents the largest “drug-like” and diverse collection of 3D structures of natural products (NPs) covering the geographical region of the entire African continent, which is readily available…

UNPD
Dataset

UNPD Universal Natural Products Database

A comprehensive resource of natural products for virtual screening. UNPD…

A comprehensive resource of natural products for virtual screening. UNPD comprises more than 220,000 molecules and their identification information (chemical name, CAS registry number, molecular…

BioPhytMol
Dataset

BioPhytMol

A manually curated drug discovery community resource on anti-mycobacterial…

A manually curated drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts. Currently, BioPhytMol holds a total of 2,582 entries including 188 plant families…

NADI
Dataset

NADI Natural Product Discovery System

Aims users to search information about biochemistry and herbs. NADI is a useful…

Aims users to search information about biochemistry and herbs. NADI is a useful resource for researchers that wish develop project on natural product and silico drug discovery.

RIKEN NPEdia
Dataset

RIKEN NPEdia RIKEN Natural Products Encyclopedia

Allows to search chemical compounds for Natural Products Encyclopedia of RIKEN.…

Allows to search chemical compounds for Natural Products Encyclopedia of RIKEN. RIKEN NPEdia includes a search engine. It offers users to search information by two ways: a simple keyword search, and…

CVDHD
Dataset

CVDHD Cardiovascular Disease Herbal Database

A comprehensive resource for virtual screening and drug discovery from natural…

A comprehensive resource for virtual screening and drug discovery from natural products isolated from medicinal herbs for cardiovascular-related diseases. CVDHD comprises 35,230 distinct molecules…

DMNP
Dataset

DMNP Dictionary of Marine Natural Products

A comprehensive database containing over 30,000 compounds. DMNP is a subset of…

A comprehensive database containing over 30,000 compounds. DMNP is a subset of the Dictionary of Natural Products (DNP) database. DNP is an ongoing project based on a 25-year review of the natural…

MarinLit
Dataset

MarinLit

A database dedicated to marine natural products research. The extremely…

A database dedicated to marine natural products research. The extremely comprehensive range of data contained along with these powerful features makes MarinLit the database of choice for marine…

AntiBase
Dataset

AntiBase

A comprehensive database of more than 40,000 natural compounds from…

A comprehensive database of more than 40,000 natural compounds from micro-organisms and higher fungi. AntiBase contains more than 400,000 biological, physical, and physicochemical data records. High…

HIT
Dataset

HIT

A comprehensive and fully curated database to complement available resources on…

A comprehensive and fully curated database to complement available resources on protein targets for FDA-approved drugs as well as the promising precursors.

TCMD
Dataset

TCMD Traditional Chinese Medicine Database

Offers information from both traditional knowledge and modern science. TCMD is…

Offers information from both traditional knowledge and modern science. TCMD is a database of Traditional Chinese Medicines. It also provides a method for 3D chemical structure transfer and display…

TCMGeneDIT
Dataset

TCMGeneDIT

Provides association information about traditional Chinese medicine (TCM),…

Provides association information about traditional Chinese medicine (TCM), genes, diseases, TCM effects and TCM ingredients mined from vast amount of biomedical literature. Integrated protein-protein…

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