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MedCrawler
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. It searches user-generated blog posts and analyzes them for correlations between medically relevant terms. It offers a method to include data from a wide variety of sources and authors, and includes automated information extraction and representation. MedCrawler can be used as a supplementary tool to support sample library design for screening campaigns or to provide a quick overview over modern folklore.
BATMAN-TCM / Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine
The first online bioinformatics analysis tool for molecular mechanism of traditional chinese medicine (TCM). BATMAN-TCM main functions include 1) TCM ingredients' target prediction; 2) functional analyses of targets including biological pathway, Gene Ontology functional term and disease enrichment analyses; 3) the visualization of ingredient-target-pathway/disease association network and KEGG biological pathway with highlighted targets; 4) comparison analysis of multiple TCMs. BATMAN-TCM will contribute to the understanding of the "multi-component, multi-target and multi-pathway" combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCM's molecular mechanism.
DisArticle
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 statistical data. It was made to discriminate between articles on traditional medicine and those of other disciplines for all articles that have both titles and abstracts in MEDLINE. The tool enables users to identify other articles besides those in MEDLINE and to obtain statistical data such as the top ten researched herbs and the top ten journals publishing the most articles on traditional medicine.
HerDing
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, chemical-gene and gene-disease relationships, which were obtained from other databases and text-mining of published articles, to find herb-disease relationships. Users of HerDing can search herbs related to a disease with an input of disease-related genes or a disease name. In addition, users can query a chemical name for retrieving herbs and genes related to the input chemical and herb names for extracting chemicals and genes related to the input herb.
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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.
GNPS / Global Natural Products Social Molecular Networking
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 NP data can be shared, analyzed, and annotated by researchers worldwide. It enables a cycle of annotation in which users curate data, continuous dereplication enables product identification, and a knowledge base of reference spectral libraries and public data sets is created.
TCM [email protected]
Gathers information about herbs, animal products and minerals listed from Chinese medical texts, dictionaries, Medline and ISI Web of Knowledge. TCM [email protected] contains more than 20000 ingredients from over 450 different herbs, animal products, and minerals TCM regimens divided into 22 drug classes based on clinical applications recorded in TCM monographs. Each entry provides the identified TCM compound(s) and the associated references, 2D/3D structures, and molecular properties.
ArachnoServer
Gathers information on the sequence, structure, function, and pharmacology of spider-venom toxins. ArachnoServer is an online database that allows advanced searches of toxin information, browsing, as well as similarity searches using BLAST. Each toxin record is displayed in a single page and a toxin's structure can be dynamically visualized. This repository introduces a bioinformatics pipeline (named Tox|Note) that automatically identifies and analyzes toxins in assembled venom-gland transcriptomes.
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.
StreptomeDB
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 addition, we have extended the background information and included hundreds of new manually curated references to literature. The latest update features a unique scaffold-based navigation system, which enables the exploration of the chemical diversity of StreptomeDB on a structural basis.
SuperToxic
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 their toxicity, based on more than 2 million measurements. The SuperToxic database provides a variety of search options like name, CASRN, molecular weight and measured values of toxicity. With the aid of implemented similarity searches, information about possible biological interactions can be gained.
FlavorDB
Integrates multidimensional aspects of flavor molecules. FlavorDB provides a comprehensive repository of flavor molecules, flavor profiles, physicochemical properties and natural sources. By bringing relevant information under a single umbrella, this online resource provides a comprehensive dataset backed by a user-friendly interface, creative visualizations, and interlinked search engines for exploring features that contribute to the sensation of flavor. It paves the way for an improved understanding of flavor perception arising out of complex interplay of flavor compounds with biological systems and allied applications.
VenomKB
New
Covers venom peptides. VenomKB contains molecular characteristics, biodiversity data, manually- and automatically identified literature data, and a standardized ontological representation for these different data types. It is useful for toxinologists, informaticians, molecular biologists, and educators interested in venoms and/or their components. This database provides a set of over 39 00 literature annotations that describes a venom or a venom component treating a disease or health condition.
CEMTDD / Chinese Ethnic Minority Traditional Drug
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 neurodegenerative disease. CEMTDD displays networks for intricate relationships between Chinese Ethnic Minority Traditional Drugs (CEMTDs) and treated diseases, as well as the interrelations between active compounds and action targets, which may shed new light on the combination therapy of CEMTDs and further understanding of their herb molecular mechanisms for better modernized utilizations of CEMTDs, especially in gerontology.
NuBBEDB / NuBBE database
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 biomes Cerrado and Atlantic Forest. It provides botanical, chemical, pharmacological, and toxicological information and includes a variety of information for each compound including chemical class and name, code, molecular formula, mass and source. A Web-based search tool allows users to search for compounds by property, chemical structure, or a combination of criteria.
SANCDB / South African natural compound database
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 database, which is simple and easy to use, while allowing for compounds to be searched by a number of different criteria. Being fully referenced, each compound page contains links to the original referenced work from which the information was obtained. Further, SANCDB provides a submission pipeline, allowing researchers to deposit compounds from their own research into the database.
BioPhytMol
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 (comprised of 692 genera and 808 species) and 633 active compounds and plant extracts identified against 25 target mycobacteria. Multiple analysis approaches have been used to prioritize the library for drug-like compounds, for both whole cell screening and target-based approaches. In order to represent the multidimensional data on chemical diversity, physiochemical properties and biological activity data of the compound library, novel approaches such as the use of circular graphs have been employed.
NPCARE / Natural Products CARE
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 plants, marine organisms, fungi, and bacteria whose anticancer activities were validated with 1107 cell lines for 34 cancer types. It can serve as a dominant gateway for the discovery of new anticancer medicines due to the inclusion of a large number of the fractional extracts as well as the natural compounds isolated from a variety of biological resources.
CHEM-TCM / Chemical Database of Traditional Chinese Medicine
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 common Western therapeutic targets, and estimated molecular activity according to traditional Chinese herbal medicine categories. It could be the most comprehensive to date attempt to connect Chinese and Western medicine on the molecular level.
3DMET / 3D-structure database 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 living cell. Atom chirality is also essential factor of the 3D-structure for molecular recognition. However, many programs of 2D-3D converters can not transform correctly about all of the natural metabolites. Thus, 3DMET has been developed.
PDTCM / Psoriasis Database of Traditional Chinese Medicine
Provides users a psoriasis database of traditional Chinese medicine with systems pharmacology-based methods. PDTCM comprises eight data entities including herbal formulas, Traditional Chinese medicine (TCM), source plants/animals, molecules, target proteins, docking results between all molecules and target proteins, diseases and clinical biomarkers. It also offers clues and ideas in exploring perspective and effective TCM for psoriasis.
AfroDb
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 for download and use in virtual screening campaigns. Virtual screening workflows usually involve docking a compound library into the binding site of a target receptor and using scoring functions and binding free energy calculations to identify putative binders. The availability of 3D structures of the compounds to be used for docking is of utmost importance. Therefore the availability of such structures within AfroDb, as well as their calculated physico-chemical properties and indicators of “drug-likeness” within this developed database will facilitate the drug discovery process from leads that have been identified from African medicinal plants.
NANPDB / Northern African Natural Products Database
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 bacteria) from Algeria, Egypt, Libya, Morocco, Sudan, South Sudan, Tunisia, Western Sahara, and parts of Northern Mali. Searches can be made by compound names, chemical substructure, compound similarity, source organism name and family, references, and compound classes and subclasses, or by keywords.
TCMGeneDIT
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 interaction and biological pathways information are also available for exploring the regulations of genes associated with TCM curative effects. In addition, the transitive relationships among genes, TCM and diseases could be inferred through the shared intermediates. Furthermore, TCMGeneDIT is useful in understanding the possible therapeutic mechanisms of TCM via gene regulations and deducing synergistic or antagonistic contributions of the prescription components to the overall therapeutic effects.
TM-MC
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 extracted manually from chromatography articles searched on MEDLINE and PubMed Central. In addition, links to PubMed are also provided to allow users to examine and review the articles from which the information has been extracted. Users are provided information on the names (Latin name, common name, Korean name, Chinese name, scientific name), photograph, effects, and treatment targets for each medicinal material. In addition, each scientific name is connected to the species on the NCBI Taxonomy and each chemical compound is connected to the chemical compound on PubChem and ChemSpider database, respectively, thus allowing users to see chemical formulas or other information provided by PubChem or ChemSpider database.
SerpentinaDB
Provides the whole Rauvolfia serpentina molecules facilitating prospection for therapeutic molecules from a medicinally important source of natural products. SerpentinaDB provides refined search option for identification of analogs of natural molecules against ZINC database at user-defined cut-off. The database can be explored for plant-derived molecules (PDMs) in a number of ways through querying the database with a simple text search tool that provides various options for searching.
TaxKB / Taxane Knowledge Base
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 natural and synthetic taxanes with a “General Search” option in addition to a “Parameter Specific Search”. It aims to provide information on Absorption, Distribution, Metabolism, and Excretion/Toxicity as well as data on bioavailability and target interaction properties of candidate anticancer taxanes, ahead of expensive clinical trials.
Traditional Chinese Medicine Drugs Information System
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 molecular information from a remote database, (ii) simple query as well as complex logic query on almost every field of a record, (iii) incremental query upon previous search, (iv) easy substructure query, (v) various display modes with many fine-tuned options for 3D structure visualization, (vi) calculation of bond distance, torsion angle, and bond angle on a 3D structure, (vii) batch 3D structures output to integrate with other commercial molecular simulation or drug design software.
EssOilDB / ESSential OIL DataBase
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. The database also includes experimentally recorded essential oil profiles from several published reports. Users can combine different parameters as environmental conditions or geographical distribution in a single search to highlight the role played by each of them in the essential oil composition of the studied plant.
Carotenoids Database
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 original papers. The original chemical fingerprints newly investigated and described here make it easy to classify chemical modification patterns in carotenoid structures, to similarity search, and to predict some of the biological functions of carotenoids such as provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity against cancer cells, and reverse multi-drug resistance (MDR) activity. The goal of the Carotenoids Database is to understand how organisms are related via carotenoids, either evolutionarily or symbiotically or in food chains through natural histories.
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 all answer to these criteria: Ayurvedic or traditional medicinal use; adequately explored for phytochemical analysis; unexplored for pleiotropic pharmacological studies. The database offers a way to explore the mechanisms of action and pharmacological effects of individual components or combinations of medicinal plants.
OliveNetTM
Gathers compounds identified from Olea europaea. OliveNetTM describes more than 600 compounds associated with O. europaea, including about 200 phenolic compounds. Users can examine their chemical structure for structure-activity relationship analyses and for potential use in virtual screening. The database can serve as a resource for those interested in compounds found within the various matrices of the olive, the associated analytical techniques used in their identification and/or isolation.
Phytochemica
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. Phytochemica was developed to facilitate prospection of therapeutic molecules from these medicinally important plants. It also offers refined search option to explore the neighbourhood of chemical space against ZINC database to identify analogs of natural molecules at user-defined cut-off. Availability of phytochemical structured dataset may enable their direct use in in silico drug discovery which will hasten the process of lead identification from natural products under proposed hypothesis, and may overcome urgent need for phytomedicines.
AntiBase
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 resolution masses for M, M+/-H, M+Na ions. The data in AntiBase have been collected from the primary and secondary literature and then carefully checked and validated. AntiBase includes descriptive data (molecular formula and mass, elemental composition, CAS registry number); physico-chemical data (melting point, optical rotation); spectroscopic data (UV, 13C-NMR, IR and mass spectra); biological data (pharmacological activity, toxicity); information on origin and isolation and a summary of literature sources. A unique feature of AntiBase is the use of predicted 13C-NMR spectra for those compounds where no measured spectra are available. These spectra have been produced using the spectrum prediction program SpecInfo.
DMNP / Dictionary of Marine Natural Products
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 product literature. For the present project, the subset of DNP entries referring to marine natural products were carefully checked and reviewed and enhanced with a considerable amount of additional information relating to their natural occurrence. Several careful reviews were also carried out to ensure that the coverage of marine natural products in the finished publication was as complete as possible.
MarinLit
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 natural products researchers. MarinLit is text and structure searchable. Queries can be built across a number of fields and parameters. Along with comprehensive information on relevant published articles and compounds, MarinLit provides dereplication tools based on experimental and predicted data.
TBC2health / Tea Bioactive Compounds
Obsolete
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 comprehensive information about a bioactive relationship that can be accessed in three aspects: (i) compound information, (ii) disease (or phenotype) information and (iii) evidence and reference. Using the curated bioactive relationships, a bipartite network was reconstructed and the corresponding network (or sub-network) visualization and topological analyses are provided for users.
CVDHD / Cardiovascular Disease Herbal Database
Obsolete
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 and their identification information (chemical name, CAS registry number, molecular formula, molecular weight, international chemical identifier (InChI) and SMILES), calculated molecular properties (AlogP, number of hydrogen bond acceptor and donors, etc.), docking results between all molecules and 2,395 target proteins, cardiovascular-related diseases, pathways and clinical biomarkers. All 3D structures were optimized in the MMFF94 force field and can be freely accessed. By using the methods of virtual screening and network pharmacology, CVDHD provides a platform to streamline drug/lead discovery from natural products and explore the action mechanism of medicinal herbs.
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