Annotated compounds; Buying small molecules

 

  • NALDB - Nucleic acid ligand database for small molecules targeting nucleic acid (2016) - database
  • DrugCentral - Online drug compendium (2016) - database
  • KLIFS - A structural kinase-ligand interaction database - database
  • PDEStrIAn - A Phosphodiesterase Structure and Ligand Interaction Annotated Database - database
  • FooDB - FooDB is the world’s largest and most comprehensive resource on food constituents, chemistry and biology. It provides information on both macronutrients and micronutrients, including many of the constituents that give foods their flavor, color, taste, texture and aroma - database
  • GLASS - GPCR-Ligand Association database - database
  • CancerResource - CancerResource-updated database of cancer-relevant proteins, mutations and interacting drugs - database
  • Metabolomics Workbench - An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools - database
  • CancerHSP - Anticancer herbs database of systems pharmacology (natural products) - database
  • SCUBIDOO - Screenable Chemical Universe Based on Intuitive Data OrganizatiOn (SCUBIDOO). 21 million virtual products originating from a small library of building blocks and a collection of robust organic reactions - database for in silico screening
  • Chemical probes - Molecular Libraries Probes (NIH probes dataset on Molsync) MLP Probes chemical probes - database
  • DrugBank - DrugBank, list of drugs, experimental structures...In 2014, many novel information about drug metabolism - database
  • EpiDBase - A manually curated database for small molecule modulators of epigenetic landscape (about 5000 cmpds in 2015) - database
  • CFam - A chemical families database based on iterative selection of functional seeds and seed-directed compound clustering (2015) - database
  • CoCoCo - It is a suite of molecular databases for high throughput virtual screening purposes - database
  • DTP - Anti-cancer Agent Mechanism Database (122 molecules) with reasonably well known mechanism of action (NCI-NIH). Development therapeutic program - database
  • EDULISS - A small-molecule database with data-mining and pharmacophore searching capabilities - database
  • HIT - Linking herbal active ingredients to targets, natural products.Derived from more than 3250 literatures, it currently contains 5208 entries about 1301 known protein targets (221 of them are described as direct targets) affected by 586 herbal compounds from more than 1300 reputable Chinese herbs, overlapping with 280 therapeutic targets from Therapeutic Targets Database (TTD), and 445 protein targets from DrugBank corresponding to 1488 drug agents. The database can be queried via keyword search or similarity search - database
  • NutriChem - NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods - database
  • Chemical probes - Molecular Libraries Probes MLP Probes - database
  • ZENODO - The ZENODO platform contains annoted compounds for several targets (Bajorath group 2014) - database
  • iSMART - It is a multi-functional cloud-computing web system that comprised with three components: (1) TCM Database@Taiwan, (2) iScreen, for virtual screening, and (3) iSplice. Natural products based on components from traditional Chinese medicines - database online
  • Pediatrics - Expanding the scope of drug repurposing in pediatrics: The Children s Pharmacy Collaborative. A database of small molecules for children in a SDF file in the supplement data - dataset to download
  • Allostery - Allosteric molecules at Chembl - dataset to download
  • Find Compounds - iScienceSearch most typical applications: For what is my compound useful? Find suppliers for lab and research chemicals. Search the AKosSamples database by substructure. Search the Internet by drawing a structure. Type a name and you get the structure. Search patents. A kind of Google for chemistry. Also ADMET information - online
  • Drug Databases - Medi-Span provides a number of clinical files or modules intended to support safety screening, clinical decision support, and other functions across healthcare applications (commercial) - database
  • NAPRALERT - A relational database of all natural products including molecules used in Ayurvedic medicine (traditional medicine, Ayurveda) - database
  • FRLHT - Foundation for Revitalisation of Local Health Traditions. Natural products including molecules used in Ayurvedic medicine (traditional medicine, Ayurveda) - database
  • Selleckchem - Chemical compounds some with numerous annotations (including preclinical data), some dedicated to targets...(Selleck Chemicals) - database online
  • TCMSP - A database of systems pharmacology for drug discovery from herbal medicines - database
  • ODORactor - An open access web server aimed at providing a platform for identifying odorant receptors (ORs) for small molecules and for browsing existing OR-ligand pairs - database - online tool
  • UniChem - Chemical structure integration across a large number of public resources - database - online
  • BARD - The powerful new bioassay database from the NIH Molecular Libraries Program - database
  • Surechem - SureChEmbl: Chemical structures from patents - database - online
  • ZINClick - A Database of 16 Million Novel, Patentable, and Readily Synthesizable 1,4-Disubstituted Triazol - database
  • SM2miR - A database of experimentally validated small molecules effects on microRNA expression - database
  • SuperScent - A database of flavors and scents - database
  • MCSS - A multi-fingerprint browser for the ZINC database. To confirm the activity of an initial small molecule hit compound from an activity screening, one needs to probe the structure–activity relationships by testing close analogs. The multi-fingerprint browser assists this process - database and search tool
  • Flavornet - Flavornet and human odor space - database
  • fragrance - Expanding the fragrance chemical space for virtual screening, SuperScent and Flavornet were analyzed to define a fragrance-like (FL) property range. Diverse collections were analyzed with this FL filter and the FL-mapplet and FL-browser were created - database
  • Orange Book - Approved Drug Products with Therapeutic Equivalence Evaluations - database
  • Drug2Gene - A knowledge base (reported 2014), which combines the compound drug-gene protein information from 19 publicly available databases - database
  • Database - PROCOGNATE is a database of protein cognate ligands for the domains in enzyme structures as described by CATH, SCOP and Pfam, and is available as an interactive website or a flat file - database
  • AnalytiCon - Analyticon Discovery GmbH: Natural product company - database online
  • EGFRIndb - Epidermal Growth Factor Receptor Inhibitor Database - database
  • SMMRNA - An interactive database with special focus on small molecule ligands targeting RNA. Currently, SMMRNA consists of 770 unique ligands along with structural images of RNA molecules - database
  • e-LEA3D - e-Drug3D: Chemical content of the collection of commercial fragments (privileged structures) extracted from the FDA approved drugs - online
  • AfroDb - A Select Highly Potent and Diverse Natural Product Library from African Medicinal Plants (about 1000 molecules) - database
  • pan-ANAPL - pan-African Natural Products Library - ask the authors, the Link does not seem to work
  • QCL - Nature Bank and the Queensland Compound Library: Unique International Resources at the Eskitis Institute for Drug Discovery - database
  • MAPS - Medicinal plant Activities, Phytochemical and Structural Database - database
  • CVDHD - A cardiovascular disease herbal database for drug discovery and network pharmacology - database
  • DNP - Dictionary of Natural Products - database
  • HEMD - An integrated tool of human epigenetic enzymes and chemical modulators for therapeutics - database
  • WebCSD - The world's online portal to the Cambridge Structural Database - database
  • Link - Collection for FBDD/FBLD : commercial fragments (privileged strutures) extracted from FDA approved drugs - database
  • HEI - A database of high energy intermediates for docking - datasets
  • BIAdb - A Database for Benzylisoquinoline Alkaloids - database
  • BitterDB - A database of about 570 bitter compounds - database
  • StreptomeDB - A resource for natural compounds isolated from Streptomyces species - database
  • NPACT - Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database - database
  • SuperNatural - A searchable database of available natural compounds (around 2015, Super Natural II, over325500 natural compounds) - database - online
  • UNPD - Universal natural products database in May 2013, about 197201 natural products from plants, animals and microorganisms - database
  • KIDFamMap - A database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms - database
  • CBID - CBLigand.org or CBID is a Web-interfaced cannabinoid molecular information database repository that are designed and constructed to facility data-sharing and information exchange among scientific research communities with online structure search functions and data analysis tools implemented - database
  • CamMedNP - Building the Cameroonian 3D structural natural products database for virtual screening, Fidele Ntie-Kang et al., BMC Complementary and Alternative Medicine 2013, contact the authors and check the supplement file. Over 2500 molecules - database
  • Xemistry - Interactive Quantitative Structure Fragmentation - online
  • Xemistry - Chemical Structure Algorithm consistency verification service - online
  • SciFinder - Provides researchers with unlimited access to the world s largest and most reliable collection of chemistry and related science information - commercial
  • Reaxys - A web-based search and retrieval system for available chemical compounds. Reaxys gathers three separate databases spanning organic chemistry, organometallic and inorganic chemistry of chemical patents, and contains reaction and substance data, as well as experimentally measured properties - commercial
  • Assistant - ScreeningAssistant 2 is a free and open-source desktop software dedicated to store and manage chemical libraries in a local or network-accessible MySQL database, and perform various analysis using simple and advanced chemoinformatics methods. Linux and Windows - Tool to prepare collection, standalone
  • SPORES - Structure PrOtonation and REcognition System - standalone
  • Link - KODE solutions istMolBase: dataset management (reading of SMILES and SDF files, depiction, molecule normalization, SMARTS matching), istChemFeat: dataset analysis by means of relevant chemical features research - standalone
  • CLEVER - Chemical library editing, visualizing and enumerating resource: tool to manage collection - standalone
  • Link - looking at SMARTS - SMARTS chemoinfo online
  • OlfactionDB - Odorants are molecules that efficiently carry chemical information, providing one of the main ways for communicating with the environment in all kingdoms of life. In the other hand, mammalian genomes codify for hundreds of olfactory receptors (OR), underlying the crucial role of the sense of smell during evolution, being able to discriminate about 10000 different odors - database
  • LIPIDMAPS - Provides a range of tools and resources to facilitate lipid research - database
  • Link - French compound collection - CNRS - database, need to register
  • AutoClick Chem - Performs many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization - standalone
  • Chemical space - ScaffoldTreeGenerator Chemoinformatics - navigation in chemical space - standalone
  • SeRAPhiC - Data set of 53 high-quality protein-fragment complexes - dataset
  • BAPPL - 161 protein-ligand complexes with experimental and estimated binding free energies - dataset
  • SMPDB - Small Molecule Pathway Database is an interactive, visual database containing more than 350 small molecule pathways found in humans - database
  • GDB-11 - Enumerates small organic molecules up to 11 atoms of C, N, O and F following simple chemical stability and synthetic feasibility rules, other related databases, peptides - virtual database online & other related tools
  • Link - Chemical structure lookup search in search in 74 million indexed structures from over 100 databases (46 million unique structures) - database
  • ClinicalTrials - A registry of federally and privately supported clinical trials conducted in the United States and around the world. ClinicalTrials.gov gives you information about a trial's purpose, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals - database
  • Link - Animal drugs - database
  • Link - FDA Animal drugs: Electronic Animal Drug Product Listing Directory - database
  • AMDD - Antimicrobial Drug Database: 2900 antibacterial and 1200 antifungal - database
  • Link - open drug database - database
  • ChemBank - Free collections and utilities, known drugs, many annotated molecules, molecules with druglike and non-druglike properties - Compound Database, Compound searching, prescription drugs online
  • PubChemDB - PubChemDB is a Java API for working with PubChem data-sets - Database online
  • PubChem - An information resource Linking chemistry and biology - Database online
  • Link - Chemical thesaurus : database including chemical entities, interactions, reactions, processes - Compound Database online
  • Link - Chemical suppliers and collections - Compound Database online
  • Link - Web directory about compound collections and many related Links, database search (bioscreening) - Compound Database, Compound searching online
  • Link - Free collections if you collaborate with the group - Compound Database, part of the French National Compound collection
  • Link - Free collections KEGG ligand database - Compound Database, online
  • Link - Crystallography Open Database - compounds in 3D, database
  • NMRShiftDB - Free collection, some molecules are in 3D - Compound Database
  • NMRShiftDB - NMRShiftDB - Compound Database
  • ZINC - Free collections (and Links to many commercial vendors), also natural products - Compound Database, ADME/Tox, Compound searching
  • DUD-E - The complete DUD-E benchmarking set, the more recent DUD, 2012 - datasets
  • DUD - DUD is designed to help test docking algorithms by providing challenging decoys - Compounds for different targets, thrombin, FXa...and decoys, datasets
  • ChemMine - Free collections and similarity search utilities, clustering - Compound Database, Compound searching, online
  • navigator - Chemnavigator: Commercial collection - Compound Database, Compound searching, online
  • ChEBI - Dictionary of small molecules. ChEBI: a database and ontology for chemical entities of biological interest - Compound Database, online
  • Link - DNA-DRUG complex dataset - Compound Database and Macromolecules
  • NuBBEDB - NuBBE database is a virtual database of natural products and derivatives from Brazilian biodiversity - Compound Database
  • BindingDB - Measured binding affinities, macromolecule-ligand complexes - Compound Database, Macromolecules, online
  • MOAD - Binding MOAD (Mother of All Databases) - Compound Database, Macromolecules, online
  • SIDER - Contains information on marketed medicines and their recorded adverse drug reactions. Profiling - profiling, ADMETox, database, online
  • STITCH - Interaction networks of chemicals and proteins. Profiling. Genomes, about 2200 drugs, 68000 chemicals - Compound Database, Macromolecules, online
  • LPDB - LPDB database: ligand-protein - Drug-Ligand Database
  • MMsINC - A database of non-redundant, richly annotated, and biomedically relevant chemical structures - Drug Database, online
  • SMILIB - Tool to create virtual libraries - Virtual Database generator in smiles, standalone
  • GLARE - Generate combinatorial library - standalone
  • Newlead - Generate of combinatorial library from bioactive conformations - standalone
  • sMOL Explorer - A 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction, and statistical analysis and data mining through Web interface. It is an open source, web-enabled database and exploration tool for Small MOLecules datasets, Bioinformatics - Data managment - Web interface small molecules
  • e-LEA3D - De novo drug design tool, drugs approved on the market - de novo screening scaffold-hopping combinatiorial library design, online
  • Ilib Diverse - Tool to create virtual drug-like libraries - Virtual Database generator, standalone
  • Link - The US National Cancer Institute collections including natural products - Compound Database
  • Link - Main chemical-structures - Compound Database, standalone
  • Link - View properties, purchase compounds - Compound Database
  • Link - View structures and data of Open NCI DB compounds - Compound Database
  • Link - Find compound properties - Compound searching
  • Link - Similarity search and other tools - Compound searching
  • ChemSpider - Compound search, find chemical vendors - Compound searching and utilities online
  • Chembl - Database of bioactive molecules - Annotated database online
  • Link - The web of chemical informatics - Chemistry blog
  • ChemExper - Find chemicals in the ChemExper Chemical Directory - online database
  • eMolecules - With eMolecules you can draw your chemical structure and instantly search millions of molecules from across the Web and from chemical suppliers worldwide. Find chemical vendors - Compound searching online
  • PDBeChem - Consistent and enriched library of ligands, small molecules and monomers that are referred as residues and hetgroups in any PDB entry - Compound Database from the PDB, Compound searching, X-ray, online
  • Ligand-Expo - Ligand-Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank - database
  • SuperLigands - A database of ligand structures derived from the Protein Data Bank with similarity searches and other tools - online
  • Link - Chemistry and biology database: numerous Links (databases, tools) valuable for drug design projects - Compound Database, macromolecules Links to programs
  • HIC-Up - HIC-Up Hetero-compound Information: Small molecules from the PDB - Compound Database from the PDB, online
  • Link - The directory of chemistry on the WWW since 1993 - Numerous chemistry Links
  • Link - Compound collection and building blocks - Compound Database online
  • Prestwick - The Prestwick Chemical Library is a unique collection of about 1120 high-purity chemical compounds (all off patent) carefully selected - Off patent compound collections for experimental testing, online
  • Spectrum - The Spectrum Collection 2000 biologically active and structurally diverse compounds from our libraries of known drugs, experimental bioactives, and pure natural products. SDF file available - Structurally diverse compounds for experimental screening and in silico work, online
  • SeqChem - Biochemicals and other natural products - Compounds for experimental screening
  • DTP - DTP maintains a repository of synthetic and natural products that have been evaluated as potential anticancer and anti-HIV agents. This repository has an historic inventory of more than 140,000 non-discreet compounds that have been submitted to DTP from a variety of sources worldwide. - Compound collections for experimental or in silico screening
  • Marvel - Marvel Library - A Collection of Over 9000 Unique Compounds - database
  • TCMGeneDIT - Database system providing association information about traditional Chinese medicines (TCMs), genes, diseases, TCM effects and TCM ingredients automatically mined from vast amount of biomedical literature - Database online, natural products
  • TCM - TCM Database Taiwan: Largest Traditional Chinese Medicine Database for Drug Screening In Silico - Ligand Database online
  • TCMID - Traditional Chinese Medicine integrative database for herb molecular mechanism analysis - Ligand Database online
  • Indian Plant - Indian Plant Anticancer Compounds Database (Ayurvedic medicine, Ayurveda). Does not seem to work - Database online (the site is moving and may not work from time to time)
  • Link - Database on pharmacophore analysis of active principles, from medicinal plants - database, server not found, thus Link to PUBMED
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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira