Chemistry

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Chemistry

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A - Z List of Chemistry Resources

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Chemical Suppliers/Catalogs

 

Material Safety Data Sheets (MSDS) Web Resources

 

Browse Chemistry Resources by Category

 

Chemical Synthesis

  • Chem Synthesis - A small, freely available, and easily searchable database of about 40,000 chemicals with references for their synthesis, and physical properties for many of the compounds.

  • Organic Syntheses - provides detailed, reliable, and carefully checked procedures for the synthesis of organic compounds. Some procedures describe practical methods for the preparation of specific compounds of interest, while other procedures illustrate important synthetic methods with general utility. Search by Keyword, or structure, or browse the annual, and collective volumes.

  • PATAI's Chemistry of Functional Groups - for the organic chemist, searchable database containing all 21 volumes of Patai's series published from 1996 to present. New content, initially 2 volumes per year, will be added. (NIH/FNLCR)

  • Reaxys - (References from 1771-; Patents from 1803-). Formerly known as Beilstein, contains enhanced access to Beilstein, Gmelin and Patent Chemistry databases. Reaxys connects validated experimental data from the three authoritative sources and provides workflow tools designed to support planning optimization in chemistry and related disciplines such as pharmacology, toxicology and ecology. It contains specific bioassay results, logPs, toxicity values, and other valuable data. Online Tutorials Available(NIH/FNLCR)?

 

Crystallography

  • RCSB Protein Data Bank - The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. About 70% of PDB structures contain ligands such as small molecules, ions, non-aqueous solvents and standard and modified amino acids and nucleotides. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.

  • Relibase - A database and discovery tool that facilitates uncovering new insights into the interactions of proteins and ligands found in the Protein Data Bank in support of drug design projects. Article

  • WebCSD - Web based interface to the Cambridge Structural Database. Article(NIH/FNLCR)

 

Drug Design

  • CADD Group's Chemoinformatics Tools and User Services - From NCI, includes Chemical Structure Lookup Service (CSLS), Enhanced NCI Database Browser 2 (article), Optical Structure Recognition (OSR), Online SMILES translator, VRML Creator for Chemical Structures and more. The NCI/CADD group is a research unit within the Laboratory of Medicinal Chemistry (LMC).

  • CanSAR - Database for cancer translational research and drug discovery. Article 1Article 2.

  • Click2Drug - From the Swiss Institute of Bioinformatics, an online Directory of Computer-Aided Drug Design Tools, many of which are free to use.

  • DockBlaster - Fully automated docking system, including self-assessment, that allows you to screen your target against subsets of small molecules from the ZINC database ArticleHelp.

  • Drug-Gene Interaction Database (DGIdb) - Search a list of genes and find known and possible drug interactions for those genes. ArticleHelp File.

  • iScreen - From the China Medical University (Taiwan), a cloud-based web server for virtual screening and de novo drug design based on the Traditional Chineese Medicine database at Taiwan. Article 1Article 2.

  • MetaDrug and Tox Hunter - Predicts possible indications, modes of action, ADME, Phase I and Phase II metabolites, and toxicity of novel compounds, as well as possible new uses for existing drugs, and displays pathway maps for the predicted modes of action, which can be overlaid with experimental data for validation. More Information. To get an account to access MetaDrug contact Alan Doss, x6249. (FNLCR only)

  • PharmaGist - a freely available web server for pharmacophore detection from an input of a set of structures of drug-like molecules that are known to bind to the receptor of interest. The pharmacophore information can then be used in virtual screening tools, such as ZINCPharmer. ArticleHelp File.

  • Relibase - A database and discovery tool that facilitates uncovering new insights into the interactions of proteins and ligands found in the Protein Data Bank in support of drug design projects. Article

  • ZINCPharmer - automatically extracts a set of pharmacophore features from an input ligand, a protein ligand complex, or from a pharmacophore definition file created by a third party software such as PharmaGist, and returns a set of purchasable compounds from the ZINC database as results.Article.

 

Drug Information

  • DrugBank - Search for drug information by structure, chemical name, brand name, or drug category, and retrieve all indexed information as well as links to other databases for more information on the drug. Learn more about DrugBank Article 1Article 2Article 3.

  • Drug Information Portal - Searches several National Library of Medicine and other government resources for information about more than 49,000 drugs in various stages of development, from those that have entered into clinical trials to those that are already approved by the FDA.

  • Drugs@FDA - Browse the A - Z list, or search by brand name, generic name or FDA application number (NDA, or ANDA, or BLA) to retrieve Patient Package Inserts, Consumer Information Sheets, Medication Guides, Label information, and approval history for drugs approved by the FDA from 1998.

  • Medscape Drug Reference - Using the simple search interface, search by drug name, or medical condition. Provides detailed drug monographs, patient handouts, dosage, uses, and warnings.

  • Pharmaprojects (Formerly Pipeline) - covers the progress of all significant new drug candidates as they enter pharmaceutical research and development programs around the world, and tracks their development from early preclinical development right up to market launch worldwide, or to discontinuation if a drug fails at any stage. A brief, one time registration is required to use this database. (NIH/FNLCR)

  • SIDER Side Effect Resource - SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information includes side effect frequency, and drug and side effect classifications, as well as links to further information, for example drug-target relations. Use side effects for drug target prediction.

 

Drug Targets

  • Known Drug Targets

  • BindingDB - a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be drug-targets with small, drug-like molecules. BindingDB also offers tools for virtual screening of candidate ligands. Learn more about BindingDB Article 1,Article 2.

  • Braunschweig Enzyme Database (BRENDA) The Comprehensive Enzyme Information System - contains functional data collected from the literature for more than 5,000 enzymes. This is the place to come if you want to find out what compounds inhibit or activate a particular enzyme, or if you just want to find out more about the activity of a given enzyme. Learn more about BRENDA article 1article 2.

  • CanSAR - Database for cancer translational research and drug discovery. Article 1Article 2.

  • CARLSBAD Database - The CARLSBAD database aggregates high-quality subsets of small molecule bioactivities, presenting them in a unified manner using a single normalized activity value, to facilitate the study of the relationships between small molecules and targets. Article.

  • ChemProt-2.0 - a freely available resource with annotated and predicted disease chemical biology interactions that can be searched by chemical name, protein, therapeutic effect, adverse drug reaction, or disease, and provides graphical displays of the results ArticleSearch HelpResults Help.

  • Drug-Gene Interaction Database (DGIdb) - Search a list of genes and find known and possible drug interactions for those genes. ArticleHelp File.

  • DrugBank - Search for drug information by structure, chemical name, brand name, or drug category, and retrieve all indexed information as well as links to other databases for more information on the drug. Learn more about DrugBank Article 1Article 2Article 3.

  • Human Epigenetic Enzyme and Modulator Database (HEMD)- A database which provides a central resource for the display, search and analysis of the structure, function, and related annotation for human epigenetic enzymes and chemical modulators focused on epigenetic therapeutics. Article,Help

  •  Ingenuity Pathways Analysis (IPA) - a web-based bioinformatics tool from Ingenuity Systems allowing researchers to search, analyze, and graphically view molecular interactions, biological functions, and diseases. This resource may also be searched by drug name to find molecular targets that a drug interacts with, or searched by target name to find compounds that are known to interact with that target. Access to IPA The NCI IPA license includes all of FNLCR. To obtain access, you must contact the NIH IT Service Desk at 301-496-4357 (6 am - 6 pm) or visit the NIH IT Service Desk website at http://itservicedesk.nih.gov. You will then be referred to the NCI Computer group, who will help you register with IPA .(NIH/FNLCR)

  • IUPHAR/BPS Guide to Pharmacology - An expert guide to pharmacological targets and the substances that act on them.

  • MATADOR: Manually Annotated Targets and Drugs Online Resource - MATADOR is a resource for direct, as well as indirect, protein-chemical interactions. Each interaction contains links to PubMed abstracts or OMIM entries that were used to deduce the interaction. Article ,Online Tutorial

  • MetaDrug and Tox Hunter - Predicts possible indications, modes of action, ADME, Phase I and Phase II metabolites, and toxicity of novel compounds, as well as possible new uses for existing drugs, and displays pathway maps for the predicted modes of action, which can be overlaid with experimental data for validation. Search by drug name to find targets of that drug; search by target to find drugs known to interact with that target. More Information. To get an account to access MetaDrug contact Alan Doss, x6249. (FNLCR only)

  • PubChem - Provides substance information, compound structures, and bioactivity data on more than 25 million small molecules, as part of NIH's Molecular Libraries Roadmap Iniative. Search by target to find compounds that have tested positive for that target; search by compound name, or structure to find targets the compound has been tested against, and to find similar structures that are available in PubChem. Learn more about PubChem Article 1Article 2.

  • RCSB Protein Data Bank - The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. About 70% of PDB structures contain ligands such as small molecules, ions, non-aqueous solvents and standard and modified amino acids and nucleotides. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.

  • SM2miR - A database of experimentally validated small molecules' effects on microRNA expression. Article

  • STITCH - The Search Tool for Interactions of Chemicals (STITCH) is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature; Article 1Article 2.

  • Predicted Drug Targets

  • Drug-Gene Interaction Database (DGIdb) - Search a list of genes and find known and possible drug interactions for those genes. ArticleHelp File.

  • PharmMapper Server- Upload a Mol2 file or SD file (2D or 3D) of a molecule with less than 100 heavy atoms and PharmMapper will return a list of potential targets for that molecule Article.

  • SEA Search Tool (SEArch) - Relates proteins based on the chemical similarity of their ligands. Article

  • SIDER Side Effect Resource - SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information includes side effect frequency, and drug and side effect classifications, as well as links to further information, for example drug-target relations. Use side effects for drug target prediction.

 

Educational

 

Handbooks

  • AntiBase 2017 Update, the Natural Compound Identifier - is available to NCI at Frederick researchers as a networked CD-ROM via the Scientific Library. AntiBase is a comprehensive database of more than 44,000 natural compounds from micro-organisms and higher fungi. AntiBase includes descriptive data; physico-chemical data; spectroscopic data; biological data; information on origin and isolation and a summary of literature sources.  AntiBase will only open in ChemBioFinder. To get ChemBioFinder installed on your computer, as part of the ChemBioOffice software package, contact x5115. For access to Antibase, please contact Alan Doss at x6249, or by e-mail at dossal@mail.nih.gov.  (FNLCR only)

  • Dictionary of Natural Products (DNP) Online - a comprehensive database of 170,000 natural products which includes names and synonyms, formulae, chemical structures, CAS Registry Numbers, extensive source data, uses and applications, physical state, melting point, boiling point, pKa, and key literature citations, searchable by text or substructure. A comprehensive type of compound classification scheme brings together compounds that are biogenetically related. DNP is restricted to 1-2 concurrent FNLCR users; please logoff after each session. If needed, a free browser plug-in is available on the left side of the screen, "Get the Plug-in." If you need assistance using this database, please feel free to call Alan Doss at x 6249.

  • PATAI's Chemistry of Functional Groups - for the organic chemist, searchable database containing all 21 volumes of Patai's series published from 1996 to present. New content, initially 2 volumes per year, will be added. (NIH/FNLCR)?

 

Literature Resources

  • Chemistry Central - From BioMed Central, open access chemistry-related research articles, published in Chemistry Central Journal, BMC journals and other open access publications.

  • EMBASE - Coverage from 1947 to present; includes EMBASE Classic; covers international drug and pharmaceutical research from over 7,600 active journals, of which nearly 2,700 are unique compared to MEDLINE. Online Tutorials Available (NIH/FNLCR)

  • Organohalogen Compounds Database - Search by author, title, or date for papers presented at the annual Dioxin Symposia from 1900 to the present.

  • Reaxys - (References from 1771-; Patents from 1803-). Formerly known as Beilstein, contains enhanced access to Beilstein, Gmelin and Patent Chemistry databases. Reaxys connects validated experimental data from the three authoritative sources and provides workflow tools designed to support planning optimization in chemistry and related disciplines such as pharmacology, toxicology and ecology. It contains specific bioassay results, logPs, toxicity values, and other valuable data. Online Tutorials Available (NIH/FNLCR)

  • SciFinder - as of 6/2012, access through accounts administered by the NIH Library. For further information, visit SciFinder: Site-Wide Access For NIH StaffOnline Tutorials Available (NIH/FNLCR)

 

Natural Products

  • ACD Labs NMR Predictors - online software for the prediction of NMR spectra, chemical shifts, and coupling constants for the following nuclei - 1H, 13C, 15N, 19F, and 31P. Chemical structures may be drawn, pasted, or imported into the program to obtain their predicted spectra. Alternatively, you may search the database for known structures using chemical shift, coupling constant, molecular weight, molecular formula, or reference information. ***Important Note: All structures searched will remain in the program's History. If you do not want others to be able to view the structures you are searching, you will need to request your own, personal account. There is no charge for having your own account, and it should allow you to access the predictors from outside of the Frederick National Laboratory for Cancer Research (FNLCR) IP range. To set up your personal account, send an e-mail to ilab@acdlabs.com . Include your full name, phone number, and address in the body of the e-mail, and "FNLCR" in the subject line. If you have any problems, contact dossal@mail.nih.gov. (FNLCR only)

  • AntiBase 2017 Update, the Natural Compound Identifier - is available to NCI at Frederick researchers as a networked CD-ROM via the Scientific Library. AntiBase is a comprehensive database of more than 44,000 natural compounds from micro-organisms and higher fungi. AntiBase includes descriptive data; physico-chemical data; spectroscopic data; biological data; information on origin and isolation and a summary of literature sources. AntiBase will only open in ChemBioFinder. To get ChemBioFinder installed on your computer, as part of the ChemBioOffice software package, contact x5115. For access to Antibase, please contact Alan Doss at x6249, or by e-mail at dossal@mail.nih.gov. (FNLCR only)

  • Dictionary of Natural Products (DNP) Online - a comprehensive database of 170,000 natural products which includes names and synonyms, formulae, chemical structures, CAS Registry Numbers, extensive source data, uses and applications, physical state, melting point, boiling point, pKa, and key literature citations, searchable by text or substructure. A comprehensive type of compound classification scheme brings together compounds that are biogenetically related. DNP is restricted to 1-2 concurrent FNLCR users; please logoff after each session. If needed, a free browser plug-in is available on the left side of the screen, "Get the Plug-in." If you need assistance using this database, please feel free to call Alan Doss at x 6249.

  • NPACT - The Naturally Occurring Plant Based Anticancerous Compound Activity Target Database (NPACT) is a freely available, manually curated database of natural compounds from plants with anti-cancerous activity. ArticleSearch Help.

  • 3DMET - a collection of predicted three-dimensional structures of naturally occuring metabolites, with universal descriptors, 2D structures and 2D descriptors, 3D structures and 3D descriptors, and conversion status for each metabolite, which should be useful in drug design, and metabolomics studies. Article

 

Nomenclature

  • IUPAC Nomenclature - Search database of International Union of Pure & Applied Chemistry (IUPAC) for recommendations on organic & biochemical nomenclature, symbols & terminology.

 

Organizations

 

Properties

  • Known Properties

  • ACD Labs NMR Predictors - online software for the prediction of NMR spectra, chemical shifts, and coupling constants for the following nuclei - 1H, 13C, 15N, 19F, and 31P. Chemical structures may be drawn, pasted, or imported into the program to obtain their predicted spectra. Alternatively, you may search the database for known structures using chemical shift, coupling constant, molecular weight, molecular formula, or reference information. ***Important Note: All structures searched will remain in the program's History. If you do not want others to be able to view the structures you are searching, you will need to request your own, personal account. There is no charge for having your own account, and it should allow you to access the predictors from outside of the Frederick National Laboratory for Cancer Research (FNLCR) IP range. To set up your personal account, send an e-mail to ilab@acdlabs.com . Include your full name, phone number, and address in the body of the e-mail, and "FNLCR" in the subject line. If you have any problems, contact dossal@mail.nih.gov. (FNLCR only)

  • AntiBase 2017, the Natural Compound Identifier - is available to NCI at Frederick researchers as a networked CD-ROM via the Scientific Library. AntiBase is a comprehensive database of more than 44,000 natural compounds from micro-organisms and higher fungi. AntiBase includes descriptive data; physico-chemical data; spectroscopic data; biological data; information on origin and isolation and a summary of literature sources. AntiBase will only open in ChemBioFinder. To get ChemBioFinder installed on your computer, as part of the ChemBioOffice software package, contact x5115. For access to Antibase, please contact Alan Doss at x6249, or by e-mail at dossal@mail.nih.gov(FNLCR only)

  • Dictionary of Natural Products (DNP) Online - a comprehensive database of 170,000 natural products which includes names and synonyms, formulae, chemical structures, CAS Registry Numbers, extensive source data, uses and applications, physical state, melting point, boiling point, pKa, and key literature citations, searchable by text or substructure. A comprehensive type of compound classification scheme brings together compounds that are biogenetically related. DNP is restricted to 1-2 concurrent FNLCR users; please logoff after each session. If needed, a free browser plug-in is available on the left side of the screen, "Get the Plug-in." If you need assistance using this database, please feel free to call Alan Doss at x 6249.

  • NIST Chemistry WebBook - Gateway to the data collection of the National Institute of Standards & Technology. Search on compounds by name, chemical formula, CAS registry number, molecular weight, or selected ion energetics and spectral properties.

  • NIST Scientific and Technical Databases - databases are included for Analytical Chemistry, Atomic and Molecular Physics, Chemical and Crystal Structure, Chemical Kinetics, Chemistry, Materials Properties, Thermophysical and Thermochemical, Atomic Spectra Databases, and others.

  • Reaxys - (References from 1771-; Patents from 1803-). Formerly known as Beilstein, contains enhanced access to Beilstein, Gmelin and Patent Chemistry databases. Reaxys connects validated experimental data from the three authoritative sources and provides workflow tools designed to support planning optimization in chemistry and related disciplines such as pharmacology, toxicology and ecology. It contains specific bioassay results, logPs, toxicity values, and other valuable data. Online Tutorials Available (NIH/FNLCR)

  • Predicted Properties

  • ACD Labs NMR Predictors - online software for the prediction of NMR spectra, chemical shifts, and coupling constants for the following nuclei - 1H, 13C, 15N, 19F, and 31P. Chemical structures may be drawn, pasted, or imported into the program to obtain their predicted spectra. Alternatively, you may search the database for known structures using chemical shift, coupling constant, molecular weight, molecular formula, or reference information. ***Important Note: All structures searched will remain in the program's History. If you do not want others to be able to view the structures you are searching, you will need to request your own, personal account. There is no charge for having your own account, and it should allow you to access the predictors from outside of the Frederick National Laboratory for Cancer Research (FNLCR) IP range. To set up your personal account, send an e-mail to ilab@acdlabs.com . Include your full name, phone number, and address in the body of the e-mail, and "FNLCR" in the subject line. If you have any problems, contact dossal@mail.nih.gov. (FNLCR only)

  • MetaDrug and Tox Hunter - Predicts possible indications, modes of action, ADME, Phase I and Phase II metabolites, and toxicity of novel compounds, as well as possible new uses for existing drugs, and displays pathway maps for the predicted modes of action, which can be overlaid with experimental data for validation. More Information. To get an account to access MetaDrug contact Alan Doss, x6249. (FNLCR only)

 

Small Molecule Libraries

  • CBL Nitric Oxide Database - Caged nitric oxide (NO) prodrugs as research tools and for use in designing advances in clinical practice.

  • ChemBank - a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG). This knowledge environment includes freely available data derived from small molecules and small-molecule screens, and resources for studying the data so that biological and medical insights can be gained. Learn more about ChemBank article 1article 2.

  • Chemical Entities of Biological Interest (ChEBI)- A database of small molecules and their biological properties, with links to pathway information, expression data, and more. Article 1article 2.

  • CPPsite - a database of experimentally validated Cell Penetrating Peptides (10-30 amino acids). Help with using CPPsite

  • NCI Database Browser Release 2 - A Web browser to the open NCI database compounds (>250,000 structures) with different kinds of output features and links to other services for continued processing.

  • PubChem - Provides substance information, compound structures, and bioactivity data on more than 25 million small molecules, as part of NIH's Molecular Libraries Roadmap Iniative. Search by target to find compounds that have tested positive for that target; search by compound name, or structure to find targets the compound has been tested against, and to find similar structures that are available in PubChem. Learn more about PubChem Article 1Article 2.

  • SM2miR - A database of experimentally validated small molecules' effects on microRNA expression. Article

  • ZINC - a free database of commercially-available compounds for virtual screening. ZINC contains over 13 million purchasable compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). Learn more about ZINC.

 

Subject Guides

  • Click2Drug - From the Swiss Institute of Bioinformatics, an online Directory of Computer-Aided Drug Design Tools, many of which are free to use.

  • Sharing Tools and Resources - A page for Collaboration among researchers.

  • VLS3D - An online collection of mostly free to use Chemoinformatics, Bioinformatics and Related Resources, organized by Dr. Bruno Villoutreix. Article.

 

Toxicology/Hazardous Chemicals

  • NIOSH Pocket Guide to Chemical Hazards - a source of general industrial hygiene information on several hundred chemicas/classes for workers, employers, and occupational health professionals.

  • ToxFAQs - From the Agency for Toxic Substances and Disease Registry (ATSDR), scroll down the page to browse the alphabetical listing for compound report sheets, or use the search box in the upper right of the page to search all content.

  • Toxic Exposome Database - From the Wishart Research Group, University of Alberta, Canada, Toxic Exposome Database combines detailed toxin data with toxin target information for more than 3,000 toxins.

  • Toxicity Reference Database (ToxRefDB) - scroll down the page to search this toxicity database provided by the U.S. Environmental Protection Agency.

  • TOXNET - Choose from any of the databases listed on the left of the screen and enter your search term in the box provided in the center of the screen. Some of the available databases are: Hazardous Substances Database (HSDB), Chemical Carcinogenesis Research Information System (CCRIS), Developmental and Reproductive Toxicology and Environmental Teratology Information Center (DART), Integrated Risk Information System (IRIS), Toxicology Excellence for Risk Assessment database (ITER); Multi-Database searches HSDB, IRIS, ITER, CCRIS, and GENE-TOX simultaneously.

 

A - Z List of Chemistry Resource

A

  • ACD Labs NMR Predictors - online software for the prediction of NMR spectra, chemical shifts, and coupling constants for the following nuclei - 1H, 13C, 15N, 19F, and 31P. Chemical structures may be drawn, pasted, or imported into the program to obtain their predicted spectra. Alternatively, you may search the database for known structures using chemical shift, coupling constant, molecular weight, molecular formula, or reference information. ***Important Note: All structures searched will remain in the program's History. If you do not want others to be able to view the structures you are searching, you will need to request your own, personal account. There is no charge for having your own account, and it should allow you to access the predictors from outside of the Frederick National Laboratory for Cancer Research (FNLCR) IP range. To set up your personal account, send an e-mail to ilab@acdlabs.com . Include your full name, phone number, and address in the body of the e-mail, and "FNLCR" in the subject line. If you have any problems, contact dossal@mail.nih.gov. (FNLCR only)

  • AntiBase 2017, the Natural Compound Identifier - is available to NCI at Frederick researchers as a networked CD-ROM via the Scientific Library. AntiBase is a comprehensive database of more than 44,000 natural compounds from micro-organisms and higher fungi. AntiBase includes descriptive data; physico-chemical data; spectroscopic data; biological data; information on origin and isolation and a summary of literature sources. AntiBase will only open in ChemBioFinder. To get ChemBioFinder installed on your computer, as part of the ChemBioOffice software package, contact x5115. For access to Antibase, please contact Alan Doss at x6249, or by e-mail at dossal@mail.nih.gov. (FNLCR only)

B

  • BindingDB - a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be drug-targets with small, drug-like molecules. BindingDB also offers tools for virtual screening of candidate ligands. Learn more about BindingDB Article 1,Article 2.

  • Braunschweig Enzyme Database (BRENDA) The Comprehensive Enzyme Information System - contains functional data collected from the literature for more than 5,000 enzymes. This is the place to come if you want to find out what compounds inhibit or activate a particular enzyme, or if you just want to find out more about the activity of a given enzyme. Learn more about BRENDA article 1article 2.

C

  • CADD Group's Chemoinformatics Tools and User Services - From NCI, includes Chemical Structure Lookup Service (CSLS), Enhanced NCI Database Browser 2 (article), Optical Structure Recognition (OSR), Online SMILES translator, VRML Creator for Chemical Structures and more. The NCI/CADD group is a research unit within the Laboratory of Medicinal Chemistry (LMC).

  • CanSAR - Database for cancer translational research and drug discovery. Article 1Article 2.

  • CARLSBAD Database - The CARLSBAD database aggregates high-quality subsets of small molecule bioactivities, presenting them in a unified manner using a single normalized activity value, to facilitate the study of the relationships between small molecules and targets. Article.

  • CASSI Search Tool - CAS Source Index (CASSI) Search Tool is a free resource that can be used to quickly look up or confirm publication titles and abbreviations of titles indexed by CAS since 1907.

  • CBL Nitric Oxide Database - Caged nitric oxide (NO) prodrugs as research tools and for use in designing advances in clinical practice.

  • ChemBank - a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG). This knowledge environment includes freely available data derived from small molecules and small-molecule screens, and resources for studying the data so that biological and medical insights can be gained. Learn more about ChemBank article 1article 2.

  • Chemical Entities of Biological Interest (ChEBI)- A database of small molecules and their biological properties, with links to pathway information, expression data, and more. Article 1article 2.

  • Chemical Online Community - To find information on chemistry related equipment and supplies, navigate the links to the left of the page. You may also sign up for free to receive weekly newsletters designed for industry professionals.

  • Chemical Structure Lookup Service - Search in 39 million indexed structures from over 80 databases (27 million unique structures). See also NCI DTP / 2D and 3D Structural Information and the CADD Group's Chemoinformatics Tools and User Services public web site.

  • Chemistry Central - From BioMed Central, open access chemistry-related research articles, published in Chemistry Central Journal, BMC journals and other open access publications.

  • ChemNavigator - Search more than 28 million unique structures from more than 300 suppliers. Free to FNLCR scientists after registering with an NIH email address. If you do not find the substance you are looking for ready-made, use the SCSORS service to get bids from thousands of companies to have the substance custom made. (NIH/FNLCR)

  • ChemProt-2.0 - a freely available resource with annotated and predicted disease chemical biology interactions that can be searched by chemical name, protein, therapeutic effect, adverse drug reaction, or disease, and provides graphical displays of the results ArticleSearch HelpResults Help.

  • Chemsoc - From the Royal Society of Chemistry, Chemsoc is for everyone interested in chemical sciences - with events, features, links, educational materials, Visual Elements Periodic Table and Timeline.

  • Chem Synthesis - A small, freely available, and easily searchable database of about 40,000 chemicals with references for their synthesis, and physical properties for many of the compounds.

  • Click2Drug - From the Swiss Institute of Bioinformatics, an online Directory of Computer-Aided Drug Design Tools, many of which are free to use.

  • CPPsite - a database of experimentally validated Cell Penetrating Peptides (10-30 amino acids). Help with using CPPsite

D

  • Dictionary of Natural Products (DNP) Online - a comprehensive database of 170,000 natural products which includes names and synonyms, formulae, chemical structures, CAS Registry Numbers, extensive source data, uses and applications, physical state, melting point, boiling point, pKa, and key literature citations, searchable by text or substructure. A comprehensive type of compound classification scheme brings together compounds that are biogenetically related. DNP is restricted to 1-2 concurrent FNLCR users; please logoff after each session. If needed, a free browser plug-in is available on the left side of the screen, "Get the Plug-in." If you need assistance using this database, please feel free to call Alan Doss at x 6249.

  • DockBlaster - Fully automated docking system, including self-assessment, that allows you to screen your target against subsets of small molecules from the ZINC database ArticleHelp.

  • Drug-Gene Interaction Database (DGIdb) - Search a list of genes and find known and possible drug interactions for those genes. ArticleHelp File.

  • DrugBank - Search for drug information by structure, chemical name, brand name, or drug category, and retrieve all indexed information as well as links to other databases for more information on the drug. Learn more about DrugBank Article 1Article 2Article 3.

  • Drug Information Portal - Searches several National Library of Medicine and other government resources for information about more than 49,000 drugs in various stages of development, from those that have entered into clinical trials to those that are already approved by the FDA.

  • Drugs@FDA - Browse the A - Z list, or search by brand name, generic name or FDA application number (NDA, or ANDA, or BLA) to retrieve Patient Package Inserts, Consumer Information Sheets, Medication Guides, Label information, and approval history for drugs approved by the FDA from 1998.

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  • EMBASE - Coverage from 1947 to present; includes EMBASE Classic; covers international drug and pharmaceutical research from over 7,600 active journals, of which nearly 2,700 are unique compared to MEDLINE. Online Tutorials Available (NIH/FNLCR)

  • eMolecules - Search more than 8 million unique chemicals from various suppliers, plus entries from NIST, PubChem and DrugBank.

  • EPA - U.S. Environmental Protection Agency

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  • Ingenuity Pathways Analysis (IPA) - a web-based bioinformatics tool from Ingenuity Systems allowing researchers to search, analyze, and graphically view molecular interactions, biological functions, and diseases. This resource may also be searched by drug name to find molecular targets that a drug interacts with, or searched by target name to find compounds that are known to interact with that target. It is also a good source of clinical trial information. Access to IPA The NCI IPA license includes all of FNLCR. To obtain access, you must contact the NIH IT Service Desk at 301-496-4357 (6 am - 6 pm) or visit the NIH IT Service Desk website at http://itservicedesk.nih.gov. You will then be referred to the NCI Computer group, who will help you register with IPA . (NIH/FNLCR)

  • iScreen - From the China Medical University (Taiwan), a cloud-based web server for virtual screening and de novo drug design based on the Traditional Chineese Medicine database at Taiwan. Article 1Article 2.

  • IUPHAR/BPS Guide to Pharmacology - An expert guide to pharmacological targets and the substances that act on them.

  • IUPAC Nomenclature - Search database of International Union of Pure & Applied Chemistry (IUPAC) for recommendations on organic & biochemical nomenclature, symbols & terminology.

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  • MATADOR: Manually Annotated Targets and Drugs Online Resource - MATADOR is a resource for direct, as well as indirect, protein-chemical interactions. Each interaction contains links to PubMed abstracts or OMIM entries that were used to deduce the interaction. ArticleOnline Tutorial

  • Medscape Drug Reference - Using the simple search interface, search by drug name, or medical condition. Provides detailed drug monographs, patient handouts, dosage, uses, and warnings.

  • MetaDrug and Tox Hunter - Predicts possible indications, modes of action, ADME, Phase I and Phase II metabolites, and toxicity of novel compounds, as well as possible new uses for existing drugs, and displays pathway maps for the predicted modes of action, which can be overlaid with experimental data for validation. Search by drug name to find targets of that drug; search by target to find drugs known to interact with that target. More Information. To get an account to access MetaDrug contact Alan Doss, x6249. (FNLCR only)

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  • NCI Database Browser Release 2 - A Web browser to the open NCI database compounds (>250,000 structures) with different kinds of output features and links to other services for continued processing.

  • NIOSH Pocket Guide to Chemical Hazards - a source of general industrial hygiene information on several hundred chemicas/classes for workers, employers, and occupational health professionals.

  • NIST Chemistry WebBook - Gateway to the data collection of the National Institute of Standards & Technology. Search on compounds by name, chemical formula, CAS registry number, molecular weight, or selected ion energetics and spectral properties.

  • NIST Scientific and Technical Databases - databases are included for Analytical Chemistry, Atomic and Molecular Physics, Chemical and Crystal Structure, Chemical Kinetics, Chemistry, Materials Properties, Thermophysical and Thermochemical, Atomic Spectra Databases, and others.

  • NPACT - The Naturally Occurring Plant Based Anticancerous Compound Activity Target Database (NPACT) is a freely available, manually curated database of natural compounds from plants with anti-cancerous activity. ArticleSearch Help.

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  • Organic Syntheses - provides detailed, reliable, and carefully checked procedures for the synthesis of organic compounds. Some procedures describe practical methods for the preparation of specific compounds of interest, while other procedures illustrate important synthetic methods with general utility. Search by Keyword, or structure, or browse the annual, and collective volumes.

  • Organohalogen Compounds Database - Search by author, title, or date for papers presented at the annual Dioxin Symposia from 1900 to the present.

  • OSHA - Occupational Safety and Health Administration (U.S. Dept. of Labor) - Includes links to OSHA regulations, hazard information bulletins and other agency memos and materials.

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  • PATAI's Chemistry of Functional Groups - for the organic chemist, searchable database containing all 21 volumes of Patai's series published from 1996 to present. New content, initially 2 volumes per year, will be added. (NIH/FNLCR)

  • Periodic Tables: A Visual Interpretation - Table of Elements - from Royal Society of Chemistry and WebElements - periodic table on the WWW.

  • PharmaGist - a freely available web server for pharmacophore detection from an input of a set of structures of drug-like molecules that are known to bind to the receptor of interest. The pharmacophore information can then be used in virtual screening tools, such as ZINCPharmer. ArticleHelp File.

  • Pharmaprojects (Formerly Pipeline) - covers the progress of all significant new drug candidates as they enter pharmaceutical research and development programs around the world, and tracks their development from early preclinical development right up to market launch worldwide, or to discontinuation if a drug fails at any stage. A brief, one time registration is required to use this database. (NIH/FNLCR)

  • PharmMapper Server- Upload a Mol2 file or SD file (2D or 3D) of a molecule with less than 100 heavy atoms and PharmMapper will return a list of potential targets for that molecule Article.

  • PubChem - Provides substance information, compound structures, and bioactivity data on more than 25 million small molecules, as part of NIH's Molecular Libraries Roadmap Iniative.Search by target to find compounds that have tested positive for that target; search by compound name, or structure to find targets the compound has been tested against, and to find similar structures that are available in PubChem. Learn more about PubChem Article 1Article 2.

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  • RCSB Protein Data Bank - The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. About 70% of PDB structures contain ligands such as small molecules, ions, non-aqueous solvents and standard and modified amino acids and nucleotides. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.

  • Reaxys - (References from 1771-; Patents from 1803-). Formerly known as Beilstein, contains enhanced access to Beilstein, Gmelin and Patent Chemistry databases. Reaxys connects validated experimental data from the three authoritative sources and provides workflow tools designed to support planning optimization in chemistry and related disciplines such as pharmacology, toxicology and ecology. It contains specific bioassay results, logPs, toxicity values, and other valuable data.Online Tutorials Available (NIH/FNLCR)

  • Relibase - A database and discovery tool that facilitates uncovering new insights into the interactions of proteins and ligands found in the Protein Data Bank in support of drug design projects. Article

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  • SciFinder - as of 6/2012, access through accounts administered by the NIH Library. For further information, visit SciFinder: Site-Wide Access For NIH Staff. Online Tutorials Available (NIH/FNLCR)

  • SEA Search Tool (SEArch) - Relates proteins based on the chemical similarity of their ligands. Article

  • Sharing Tools and Resources - A page for Collaboration among researchers.

  • SIDER Side Effect Resource - SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information includes side effect frequency, and drug and side effect classifications, as well as links to further information, for example drug-target relations. Use side effects for drug target prediction.

  • STITCH - The Search Tool for Interactions of Chemicals (STITCH) is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature; Article 1Article 2.

  • SM2miR - A database of experimentally validated small molecules' effects on microRNA expression. Article

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  • 3DMET - a collection of predicted three-dimensional structures of naturally occuring metabolites, with universal descriptors, 2D structures and 2D descriptors, 3D structures and 3D descriptors, and conversion status for each metabolite, which should be useful in drug design, and metabolomics studies. Article

  • ToxFAQs - From the Agency for Toxic Substances and Disease Registry (ATSDR), scroll down the page to browse the alphabetical listing for compound report sheets, or use the search box in the upper right of the page to search all content.

  • Toxic Exposome Database - From the Wishart Research Group, University of Alberta, Canada, Toxic Exposome Database combines detailed toxin data with toxin target information for more than 3,000 toxins.

  • Toxicity Reference Database (ToxRefDB) - scroll down the page to search this toxicity database provided by the U.S. Environmental Protection Agency.

  • TOXNET - Choose from any of the databases listed on the left of the screen and enter your search term in the box provided in the center of the screen. Some of the available databases are: Hazardous Substances Database (HSDB), Chemical Carcinogenesis Research Information System (CCRIS), Developmental and Reproductive Toxicology and Environmental Teratology Information Center (DART), Integrated Risk Information System (IRIS), Toxicology Excellence for Risk Assessment database (ITER); Multi-Database searches HSDB, IRIS, ITER, CCRIS, and GENE-TOX simultaneously.

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  • VLS3D - An online collection of mostly free to use Chemoinformatics, Bioinformatics and Related Resources, organized by Dr. Bruno Villoutreix. Article.

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  • WebCSD - Web based interface to the Cambridge Structural Database. Article(NIH/FNLCR)

  • WebElements - The periodic table on the WWW.

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  • ZINC - a free database of commercially-available compounds for virtual screening. ZINC contains over 13 million purchasable compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). Learn more about ZINC.

  • ZINCPharmer - automatically extracts a set of pharmacophore features from an input ligand, a protein ligand complex, or from a pharmacophore definition file created by a third party software such as PharmaGist, and returns a set of purchasable compounds from the ZINC database as results.Article.

 

Chemical Suppliers/Catalogs

  • Argus Chemicals

  • Chemical Online Community - To find information on chemistry related equipment and supplies, navigate the links to the left of the page. You may also sign up for free to receive weekly newsletters designed for industry professionals.

  • ChemNavigator - Search more than 28 million unique structures from more than 300 suppliers. Free to FNLCR scientists after registering with an NIH email address. If you do not find the substance you are looking for ready-made, use the SCSORS service to get bids from thousands of companies to have the substance custom made. (NIH/FNLCR)

  • Dow Chemicals

  • DuPont

  • eMolecules - Search more than 8 million unique chemicals from various suppliers, plus entries from NIST, PubChem and DrugBank.

  • Fisher Scientific Internet Catalog

  • Reaxys - Search for compounds by structure, properties, journal citation, name, or other chemical identifier. If a vendor for a compound is known, a Red Flask icon will appear beneath the compound's structure in the results set. Click the Red Flask, select the e-Molecules link, then click the big red Check Prices button to compare prices. Online Tutorials Available (NIH/FNLCR)

  • SciFinder - Search for compounds by structure, journal citation, name, or other chemical identifier. On the results page for any substance, click the Orange Flask with the Yellow Price Tag to find suppliers for that compound. To apply for account access, visit SciFinder: Site-Wide AccessOnline Tutorials Available (NIH/FNLCR)

  • Sigma-Aldrich Chemical Company

  • WWW Chemicals - Includes chemical catalogs, chemical equipment, chemical companies directory; structure searching available.

  • ZINC - a free database of commercially-available compounds for virtual screening. ZINC contains over 13 million purchasable compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). Learn more about ZINC.