Chemical Biology

General

• What is Chemical Biology?
• What is Chemical Genetics?

• Biochemistry Online: An Approach Based on Chemical Logic - Biochemistry within the framework of chemical principles and logic. (Henry Jakubowski, College of St. Benedict/St. John's University)
  • New Methods in Drug Development
  • Review of Organic Chemistry
• Chemie.De: The Chemistry Information Service - Searchable descriptions of chemical products, companies, news, chemicals, jobs, literature, software and events, as well as chemical resources such as chemical acronym, German/English and English/German scientific dictionaries and various online chemical tools. (Chemie.DE Information Service, Germany)
• Chemical Reactivity - Characteristic reactions of functional groups. (William Reusch, Michigan State University)
• Chem-Online.org - Information on a range of chemicals, including biochemicals, vitamins, amino acid, pharmaceuticals and plant extracts.
• ChemWeb - Resources for the chemical community.
• CombiChem.net - Portal for news and resources on combinatorial chemistry and medicinal chemistry.
• CombiChemLab News, information and links in drug discovery, combinatorial chemistry, high-throughput synthesis, high- and ultra-high-throughput screening (HTS and uHTS) and lab automation. (Guillermo A. Morales)
• Combinatorial Chemistry Review - An overview of combinatorial synthesis, including polymers and linkers for solid-phase synthesis, determination of product structure, solution-phase synthesis and applications of combinatorial chemistry.
• The Combinatorial Index - Web site that accompanies The Combinatorial Index with an outline of the book, links to combinatorial chemistry sites and companies.
• Diversity Information Pages - Resource for articles, patents, symposia, companies and organizations in molecular diversity.
• Drug Discovery Online - A "digital marketplace for the drug development industry" that also has current news and discussion forums.
• The Home Page for Chemists - 1223 links about chemistry.
• HHMI BioInteractive - What is Chemical Genetics? (Howard Hughes Medical Institute)
• ICCB-ICG > Screening > FAQ - HTS Facility - Information on how to set up an academic high-throughput screening facility. (Institute of Chemistry and Cell Biology - Initiative for Chemical Genetics, Harvard Medical School and National Cancer Institute)
• International Union of Pure and Applied Chemistry (IUPAC) Nomenclature Home Page - Recommendations on chemical nomenclature, symbols and terminology.
• Ionization Methods in Mass Spectrometry (JEOL USA)
• Molecules with Silly or Unusual Names (University of Bristol, UK)
• NetSci's Science Center - Dated but still useful collection of articles on combinatorial and computational chemistry and high-throughput screening.
  • The Chemical Generation of Molecular Diversity - Overview of diversity generation in combinatorial chemistry (diversity-oriented synthesis) describing pin technology, split-pool synthesis, iterative deconvolution, encoded libraries, phage libraries, peptoid libraries etc. (Michael R. Pavia, Sphinx Pharmaceuticals, 1995)
  • Statistical Considerations in High Throughput Screening - "This paper focuses on some of the issues we have found useful to think about with regard to data analysis when designing high-throughput biochemical assays." (Michael W. Lutz et al., Glaxo-Wellcome Research Institute, 1996)
• New Methods in Drug Development - Basic overview with links to topics in drug development, combinatorial chemistry, in situ click chemistry, chemical genetics, DNA- and RNA-binding drugs, multivalency and inhibitor design and targeting drugs to cancer cells. (Part of Biochemistry Online: An Approach Based on Chemical Logic, Henry Jakubowski, College of St. Benedict/St. John's University)
• O=CHem Directory - Basic organic chemistry lessons and tables of data. (University of Southern Maine)
• Organic Chemistry Portal - General portal and resource, with tools such as OSIRIS, which calculates drug-relevant properties of chemical structures (cLogP, solubility, etc.).
• Protein Idenfitication and Sequencing Using Mass Spectrometry Data - Slide-based lesson covering the use of MALDI-TOF, tandem MS, etc. in protein science.
• Royal Society of Chemistry's Chemical Science Network
• Small Molecule Drug Metabolism - Short tutorial on the detoxification of xenobiotics. (Walter Yu, Celera Corp.)
• Virtual Textbook of Organic Chemistry (William Reusch, Michigan State University)
• Wikipedia - Free online encyclopedia with basic overviews. (Beginner's Level)
  • Biotechnology
  • Cheminformatics
  • Combinatorial Chemistry
  • Computational Chemistry
  • Drug
  • Drug Design
  • Drug Discovery
  • Medicinal Chemistry
  • Organic Chemistry
  • Pharmacology
  • Pharmacy
  • Quantitative Structure-Activity Relationships (QSAR)
• WWW Virtual Library of Chemistry

Chemical, Pharmacological and Small-Molecule Bioactivity Databases

• Biocatalysis/Biodegradation Database - "Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds." (University of Minnesota)
• ClinicalTrials.gov - Information in clinical trials and human research studies. (National Library of Medicine, National Institutes of Health)
• CAS, Chemical Abstracts Service - "CAS provides pathways to published research in the world's journal and patent literature--virtually everything relevant to chemistry plus a wealth of information in the life sciences and a wide range of other scientific disciplines--back to the beginning of the 20th century."
• ChemBank - Chemical structure and biological activity database. (Institute of Chemistry and Cell Biology at the Harvard Medical School, Broad Institute Chemical Biology Program, National Cancer Institute's Initiative for Chemical Genetics)
• Chemical Acronyms (Purdue University)
• Chemical Acronyms Database (Indiana University)
• ChemFinder.com - Chemical database. (CambridgeSoft)
• Cheminformatics.org - "This website contains links to cheminformatics programs and QSAR datasets (with structures!). All programs should be free to use, at least for academics."
• CHEMnetBase - Chemical databases. (Chapman & Hall/CRC Press)
• Common Molecules Collection - Information on and structures of a range of small molecules. (Reciprocal Net, Indiana University)
• DTP Datawarehouse Index - Database of the National Cancer Institute's Developmental Therapeutics Program compounds.
• Elisa Data Exchanger (EDE) - A "tool to facilitate management of experimental results from chemical screenings." Freely available online (login: evalede, password: loginede). See Leblanc et al. 2004. Biotechniques. 37:223. (Université de Montpellier, France)
• eMolecules - Search for information on and suppliers of chemicals.
  • Cheminformatics 101
• International Union of Pure and Applied Chemistry (IUPAC) - Recommendations on organic and biochemical nomenclature, symbols and terminology.
  • Basic Terminology of Stereochemistry
  • Glossary of Class Names of organic compounds and reactive intermediates based on structure.
• KEGG LIGAND Database - Database of "chemical reactions involving metabolites and other biochemical compounds, as well as xenobiotic compounds." (Kyoto Encyclopedia of Genes and Genomes)
• National Cancer Institute Computer-Aided Drug Deisgn Group's Chemoinformatics Tools and User Services
  • Chemical Structure Lookup Service
  • Online SMILES Translator and Structure File Generator
• National Center for Biotechnology Information (NCBI) (National Library of Medicine, National Institutes of Health)
  • Entrez - A retrieval system for searching the following databases
    • PubChem BioAssay - "The PubChem BioAssay Database contains bioactivity screens of chemical substances described in PubChem Substance"
    • PubChem Compound - "The PubChem Compounds Database contains validated chemical depiction information provided to describe substances in PubChem Substance."
    • PubChem Substance - "The PubChem Substances Database contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay. If the contents of a chemical sample are known, the description includes links to PubChem Compound."
  • PubChem - Gateway to PubChem, three linked databases above searchable through Entrez.
• National Library of Medicine - Specialized Information Services
  • Chemical Information
    • ChemIDplus - "A searchable database of 360,000+ chemical substance records."
    • NCI-3D Database
  • Toxicology and Environmental Health Information
    • Toxicology Tutorials
    • TOXNET - A "cluster of databases on toxicology, hazardous chemicals, and related areas."
• National Institute of Standards and Technology
  • Fundamental Physical Constants
  • NIST Chemical WebBook - Chemical database.
  • NetSci Small Molecule Resources
• NIMH/SNIDD Tracer Database - MRI tracer database: "The goal of this effort is to promote the use of imaging probes in preclinical and clinical research and in drug discovery to accelerate the identification and validation of novel targets for therapeutic intervention in human diseases, especially those with central nervous system components." (National Institute of Mental Health and the Society for Non-Invasive Imaging in Drug Development)
• Optical Properties Spectra
• PharmGKB - An "integrated resource about how variation in human gene leads to variation in our response to drug." (Stanford University)
• Periodic Table of the Elements (EnvironmentalChemistry.com)
• Periodic Table of the Elements (Los Alamos National Laboratory)
• Periodic Table of the Elements (Royal Society of Chemistry's chemsoc.org)
• Pharmabase - A database of cellular physiology and pharmacology. "This NIH funded database has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds in cellular research." (Marine Biological Laboratory, Woods Hole)
• Properties and Toxicities of Organic Solvents
• Psychoactive Drug Screening Program (PDSP) K_i Database - "The PDSP K_i database is a unique resource in the public domain which provides information on the abilities of drugs to interact with an expanding number of molecular targets. The K_i database serves as a data warehouse for published and internally-derived K_i, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes." (PDSP, Bryan Roth, University of North Carolina, Chapel Hill, and the National Institute of Mental Health)
• Small Molecule Interaction Database (SMID) - "SMID is an expanding database of small molecule - domain interactions determined from [Molecular Modeling DataBase (MMDB)] records."
• Thomson ISI Index Chemicus

Specific Molecules and Reactions

• Carbodiimide Coupling using EDC - Mechanism and information on activation of carboxylic acids using 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide and N-hydroxysuccinimide for subsequent reaction with amines to form amides, a frequently used coupling reaction. (Eugenii Katz, Hebrew University of Jerusalem, Israel)

Nucleic Acid, Gene and Genomics Databases

Protein and Proteomics Databases

Carbohydrate Databases

Lipid Databases

Enzyme Databases (Collections of Enzyme Functional and Nomenclature Data)

Macromolecular Structure Databases

Discussion Groups

• BioChemWeb.org Discussion Board - Discussions and questions/answers for scientists and students.

• Usenet newsgroup archives
  • BIOSCI/bionet (can also be accessed through Google Groups: bionet); see also individual subject pages for newsgroups on more specific topics.
    • MOLREPS/bionet.molecules.repertoires - Generation and use of libraries of molecules.
    • TOXICOL/bionet.toxicology - Research in toxicology.
  • Google Groups: sci.chem
  • Google Groups: sci.chemistry

Labs Studying Chemical Biology