Biochemistry and Molecular Biology Resources on the Web
This page is intended to provide a relatively short list of links to some of the most useful Biochemistry/Molecular Biology resources and starting points on the web. This page is always under construction... If you have any suggestions for links to add, or remove, or comments on the organization of this list, please let me know.Table of contents
Tools
Databases
Biochemistry and molecular biology centers
Information/education centers
On-line Biochemistry books and tutorials
Other
- Tools (on-line services)
- Swiss-PDB Viewer
- Easy to use and free graphics program to look at, analyse and superimpose protein 3D structures
- ExPASy tools menu
- This ExPASy page gives you access to a large collection of protein analysis tools, including, but not limited to, protein identification tools, DNA-to-protein translation, sequence similarity searches, pattern searches etc, etc.
- Pedro's BioMolecular Research Tools
- A large collection of WWW links to information and services useful to molecular biologists.
- EMBL WWW Services
- Links to many useful computational tools developed and offered by EMBL.
- BLAST
- Sequences similarity search using the Basic Local Alignment Search Tool.
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- Databases
- Entrez Browser
- Using the Entrez Browser, provided by the NCBI, you can search protein and nucleic acid databases, the Protein Data Bank of macromolecular 3D structures, genome databases, taxonomy databases, and the MedLine litterature database. Often a very good place to start looking for information.
- Medline
- Online litterature database for the life sciences.
- Protein Data Bank (PDB)
- The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The Protein Data Bank is operated by the Research Collaboratory for Structural Bioinformatics (RCSB). The PDB can also be accessed through the mirror sites at Rutgers University, National Institute of Standards and Technology, National University of Singapore, Osaka University, Japan or Universidade Federal de Minas Gerais, Brazil.
- GenBank
- GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. There are approximately 3,400,000,000 bases in 4,610,000 sequence records as of August 1999. GenBank is part of the International Nucleotide Sequence Database Collaboration, which is comprised of the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis.
- EMBL Nucleotide Sequence Database
- The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences collected from the scientific literature and patent applications and directly submitted from researchers and sequencing groups. Data collection is done in collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ).
- Swiss-Prot
- The SWISS-PROT Protein Sequence Database is a database of protein sequences produced collaboratively by Amos Bairoch (University of Geneva) and the EMBL Data Library. The data in Swiss-Prot are derived from translations of DNA sequences from the EMBL Nucleotide Sequence Database, adapted from the Protein Identification Resource (PIR) collection, extracted from the literature and directly submitted by researchers. It contains high-quality annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc), is non-redundant, and cross-referenced to several other databases, notably the EMBL nucleotide sequence database, PROSITE pattern database and PDB.
- Protein Identification Resource (PIR)
- The Protein Identification Resource consists of an integrated computer system composed of a number of protein and nucleic acid sequence databases and software designed for the identification and analysis of protein sequences and their corresponding coding sequences. The PIR serves the scientific community through on-line access, distributing magnetic tapes, and performing off-line sequence identification services for researchers.
- PROSITE
- PROSITE is a method for determining the function of uncharacterized proteins translated from genomic or cDNA sequences. It consists of a database of biologically significant sites, patterns and profiles that help to reliably identify to which known family of protein (if any) a new sequence belongs.
- Structural Classifiaction of Proteins (SCOP)
- Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The scop database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
- ENZYME
- ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
- On-line Mendelian Inheritance in Man (OMIM)
- This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information, pictures, and reference information. It also contains copious links to NCBI's Entrez database of MEDLINE articles and sequence information.
- What Is There? (WIT)
- The WIT is a resource to examine and model biochemical pathways and regulatory circuits in a variety of different organisms and cell types.
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- Biochemistry & molecular biology centers
- ExPASy
- The ExPASy World Wide Web (WWW) molecular biology server of the Geneva University Hospital and the University of Geneva is dedicated to the analysis of protein and nucleic acid sequences as well as 2-D PAGE. Top page contains, among other things, links to a number of useful databases and tool collections.
- EMBL (European Molecular Biology Laboratory)
- The European Molecular Biology Laboratory (EMBL) was established in 1974 and is supported by 14 European countries and Israel. EMBL consists of a main Laboratory in Heidelberg (Germany) and three Outstations in Hamburg (Germany), Grenoble (France) and Hinxton (Great Britain). The current research activities of the main Laboratory are carried out in four main Research Programmes, each consisting of several independent groups focussing on a specific area of molecular and cell biology. EMBL is also a teaching and training centre for the new generation of molecular biologists.
- European BioInformatics Institute (EBI)
- The EBI is an Outstation of EMBL located at Hinxton Hall,Ýnear Cambridge in the United Kingdom. The EBI maintains the EMBL and SWISS-Prot databases asÝwell as various other databases such as IMGT, NDB, PDB, Flybase and RHDB. The major databases can be queried and similarity searches can be done with FASTA and BLITZ.
- National Center for Biotechnology Information (NCBI)
- NCBI's mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. NCBI provides the Entrez Browser and also builds, maintains and distributes the GenBank Sequence Database.
- Amos' WWW links page
- This list from Amos Bairoch (father SWISS-PROT, Basel, Switzerland) features a large collection of links (sorted by subject) to biochemistry and molecular biology databases and other resources. You'll want to come back frequently to this well-kept and well-designed site.
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- Information/education centers
- BioTech
- This superb site from Indiana University aptly describes itself as "An Interactive Educational Resource and Biotechnology Reference Tool." A real treasure trove!
- Biotechnology Information Center
- The Biotechnology Information Centre at the National Agricultural Library, Agricultural Research Service, U. S. Department of Agriculture provides access to a variety of information services and publications covering many aspects of agricultural biotechnology.
- Access Excellence
- Access Excellence is a national (US) educational program sponsored by Genentech, Inc., that puts high school biology teachers in touch with their colleagues, scientists and critical sources of new scientific information through an online network. This top-class site is a must-see!
- Access Exellence list of biotech Websites
- This page features a good collection of Biotechnology web sites. An excellent starting point for further exploration.
- BioChemNet
- A directory of biology and chemistry educational resources, organized in different categories. Some of the links appear to be dead, and sometimes it's hard to understand the connection between the text in the link and what's actually on the page. Still, some useful stuff can be found here.
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- On-line Biochemistry books and tutorials
- Principles of Biochemistry
- Web companion to the book by Horton et al. 3rd edition. Not fully developed yet, but contains multiple choice questions with direct feedback that might be useful. (The webcompanion to the previous 2nd edition is also available).
- Biochemistry, van Holde
- Webcompanion for 3rd edition of Biochemistry by Mathews and van Holde.
- PPS - Principles of Protein Structure Using the Internet
- This course, hosted by Birkbeck College (London, UK), and given in collaboration with a large number of tutors throughout the world, is definitely one of the best examples around of a web-based course. Check it out!
- BiochemTeach@SU
- There are some really nice examples of web-based assignments and tutorials at this well designed teaching site from the Department of Biochemistry at Stockholm University.
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- Other
- Periodic Table of the Elements
- Well-designed, clickable Peridoc Table of the Elements from Los Alamos National Laboratory.
- Life Science Dictionary from BioTech
- This illustrated glossary contains over 5500 life science terms (February 1997). Because this resource is still very much under construction, most of the terms are associated with biochemistry, biotechnology, botany, cellular biology and genetics, but the dictionary also contains chemistry, ecology, medicine, pharmacology and toxicology terms.
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Page updated 2002.08.28 by jerry@xray.bmc.uu.se