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Chemistry Research Resources

This guide includes Chemistry Research Resources.

Chemistry Resources by Category

 

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.

  • 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 Chemical Biology Laboratory.

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

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

  • 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. Article, Help File.

  • 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 1, Article 2, Article 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 1, article 2.

  • CanSAR - Database for cancer translational research and drug discovery. Article 1, Article 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 Article, Search Help, Results Help.

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

  • 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 1, Article 2, Article 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 NCI At Your Service. (NIH/FNLCR)

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

  • 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 Initiative. 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 1, Article 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 1, Article 2.

  • Predicted Drug Targets

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

  • 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: SpringerOpen- Open access chemistry-related research articles, published in Chemistry Central Journal 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 Staff. Online Tutorials Available (NIH/FNLCR)

 

Natural Products

  • 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. (NIH/FNLCR)

  • 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. Article, Search Help.

 

Nomenclature

  • IUPAC Nomenclature - Learn about recommendations from the International Union of Pure & Applied Chemistry (IUPAC) on organic & biochemical nomenclature, symbols & terminology.

 

Organizations

 

Properties

  • Known Properties

  • 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. (NIH/FNLCR)

  • 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.

  • 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

  • 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

  • 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 1, article 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 1, article 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 Initiative. 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 1, Article 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 chemicals/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.

 

Chemical Suppliers/Catalogs

  • Chemical Online Community - Find information on chemistry related equipment and supplies, and 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 Access. Online 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.