Selected Web Sites in Biochemistry,  Molecular Biology, and Biotechnology

General and Index Sites

Research Tools, Genome Databases and Support Sites

Educational Sites

Professional Society Sites

Dictionaries and Encyclopedias

General and Index sites

Yahoo Biochemistry
http://dir.yahoo.com/Science/Chemistry/Biochemistry/

Yahoo Chemistry
http://dir.yahoo.com/Science/Chemistry/

PubMed
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed

PubMed is a freely available version of the MEDLINE index to medical literature produced by the National Library of Medicine.

Protocol Online
http://www.protocol-online.org/

This site indexes and links to web sites that provide laboratory protocols in a number of biological fields including biochemistry, bioinformatics, cell biology, genetics, genomics, and molecular biology. 

BioVisa.net
http://biovisa.net/index.php3

This research scientist managed site collects links to useful information sharing sites such as over 2000 free research protocols, a list of 1600 electronic journals, free ebooks and online discussion forums.

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 Research Tools, Genome Databases and Support Sites

eMolecules Chemical Search
http://www.emolecules.com/index.htm

A free search site produced by chemists that allows chemical structure searching, substructure searching, and name searching.

ExPASy Molecular Biology Server
http://us.expasy.org/ 

"The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures." ^*  It includes eight separate molecular biology and biochemical databases, nine proteomics and sequence analysis tools and software for 2-D Page analysis.

National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov/

"Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease."  It includes the results of the Human Genome Project and the full human genome sequence.  It also includes The NCBI Handbook, an online guide to the use of NCBI resources.

Entrez Search and Retrieval System
http://www.ncbi.nlm.nih.gov/Entrez/

This is the main entry point for the NCBI databases. "Entrez is a search and retrieval system that integrates information from several linked databases at NCBI. These databases include nucleotide sequences, protein sequences, macromolecular structures, whole genomes, and MEDLINE, through PubMed."

Entrez Nucleotides
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide

"Entrez Nucleotides database is a collection of sequences from several sources, including GenBank, RefSeq, and PDB. The number of bases grows at an exponential rate."  It includes the Draft Human Genome which is being continuously refined.

The Institute for Genomic Research
http://www.tigr.org/

"The Institute for Genomic Research (TIGR) is a not-for-profit research institute whose primary research interests are in structural, functional and comparative analysis of genomes and gene products from a wide variety of organisms including viruses, eubacteria (both pathogens and non-pathogens, archaea (the so-called third domain of life), and eukaryotes (plants, animals, fungi and protists such as the malarial parasite)."

National Center for Genome Resources
http://www.ncgr.org/

"The National Center for Genome Resources, a non-profit, bioinformatics research center, has devoted itself to pursuing research in the scientific community and catalyzing collaborative projects that contribute to improvements in agriculture, health, and the quality of life.  NCGR continues to contribute to bioinformatics and computational systems biology research by offering free downloadable software to the scientific community.  NCGR's programs in Bioinformatics and Computational Systems Biology have produced a number of software tools that are freely available to the scientific community and for those at nonprofit institutions. "

The Genome Database
http://www.gdb.org/

Molecular Biology Protocols
http://micro.nwfsc.noaa.gov/protocols/protocols.html

American Type Culture Collection
http://www.atcc.org/

Blocks WWW Server
http://blocks.fhcrc.org/

"A service for biological sequence analysis at the Fred Hutchinson Cancer Research Center in Seattle, Washington, USA.  Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. Block Searcher, Get Blocks and Block Maker are aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks (current version), retrieve blocks, and create new blocks, respectively."

Protein Data Bank
http://www.rcsb.org/pdb/

"Protein Data Bank (PDB), the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. ... The Protein Data Bank is operated by Rutgers, The State University of New Jersey; the San Diego Supercomputer Center at the University of California, San Diego; and the Center for Advanced Research in Biotechnology of the National Institute of Standards and Technology -- three members of the Research Collaboratory for Structural Bioinformatics (RCSB). "

Biosequence Comparisons -- Methods and strategies
http://twod.med.harvard.edu/seqanal/

This collection by K. Robinson of Harvard University consists of "hypertext documents that are intended to summarize the basic workings and concepts behind some popular programs, as well as to point out necessary cautions."

National Human Genome Research Institute
http://www.genome.gov/

"The National Human Genome Research Institute led the Human Genome Project for the National Institutes of Health, which culminated in the completion of the full human genome sequence in April 2003.  Now, NHGRI moves forward into the genomic era with research aimed at improving human health and fighting disease."

COPE: Cytokines Online Pathfinder Encyclopaedia
http://www.copewithcytokines.de/

This prolific site by Prof. Dr. Horst Ibelgaufts includes a 10000+ entry online dictionary that updates The dictionary of Cytokines and  19,000+ references on cytokines and related topics.

Database of Macromolecular Movements
http://molmovdb.mbb.yale.edu/molmovdb/

"Database of Macromolecular Movements with Associated Tools for Geometric Analysis.  This describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis."

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 Educational Sites

BioBioWiki
http://bbwiki.tamu.edu/index.php?title=Main_Page

The BioBioWiki by the Department of Biochemistry and Biophysics of Texas A&M University includes many educational resources including a biochemistry glossary, lab safety guide, reagent preparation guide, a guide to careers in biochemistry, a list of common abbreviations, and course related materials.

 
BioTech
http://biotech.icmb.utexas.edu/

BioTech is a hybrid biology and chemistry education resource and research tool produced by the BioTech Resources Web Project of the University of Texas Institute for Cellular and Molecular Biology and the Indiana Institute for Molecular and Cellular Biology.

NetBiochem
http://www-medlib.med.utah.edu/NetBiochem/NetWelco.htm

A site produced for the National Library of Medicine that contains tutorials on topics in medical biochemistry, tables on metabolism and illustrations of metabolic concepts.

Glossary of Biochemistry and Molecular Biology
http://www.portlandpress.com/pp/books/online/glick/search.htm

This is a free online version of this dictionary produced by Portland Press.

INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY -- Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology
http://www.chem.qmw.ac.uk/iupac/

The web site of the ultimate authority in chemical nomenclature, it includes the text of glossaries and  definition documents for most classes of organic chemicals.

Metabolic Pathways of Biochemistry
http://www.gwu.edu/~mpb/

This site contains 2D and 3D graphical representations of major human biochemical metabolic pathways.

The Biology Project
http://www.biology.arizona.edu/

This educational site by The University of Arizona includes activities, problem sets and tutorials on biochemistry, cell biology, immunology, Mendelian genetics and molecular biology.

National Human Genome Research Institute -- Educational Resources
http://www.genome.gov/Education/

The educational section of the NHGRI site has an extensive tutorial on The Human Genome Project, genetic education modules for K-12 teachers, a talking glossary of genetic terms and fact sheets on genetic concepts and research techniques.

actionbioscience.org
http://www.actionbioscience.org/

This educational website includes topical collections of full text peer reviewed articles at the high school and undergraduate level in seven fields of the biosciences including genomics and biotechnology.

BioInteractive (HHMI)
http://www.hhmi.org/biointeractive/index.html

This multimedia rich educational site by the Howard Hughes Medical Institute (HHMI) has a collection of biological,  genomic and chemical genetics, and medical educational materials including animations, biotechnology virtual lab sessions, on-demand webcast lecture series, and video clips.  It also produces a companion site DNA Interactive that celebrates the 50th anniversary of the discovery of DNA with a wealth of educational materials on DNA and genomics.

The Molecules of Life
http://biop.ox.ac.uk/www/mol_of_life/Molecules_of_Life.html

This educational site by the Laboratory of Molecular Biophysics at the University of Oxford provides an interactive introduction to the processes used to determine the structure of proteins. 

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 Professional Society Sites

chemistry.org  American Chemical society
http://www.acs.org/

This is the main portal site for ACS members, educators and students, policy makers and general chemical enthusiasts.  It includes a customizable personal portal.

Biological Chemistry Division, American Chemical Society
http://lysine.pharm.utah.edu/acsbio/acsbio.html

Royal Society of Chemistry
http://www.rsc.org/

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^* Note: Annotations in quotation marks were copied from the corresponding web site.

 Dictionaries and Encyclopedias

CHEMnetBase

CHEMnetBase is a collection of databases and electronic versions of CRC handbooks and dictionaries that include:

·         Handbook of Chemistry and Physics

·         Combined Chemical Dictionary which includes all the entries from the following:

o    Dictionary of Organic Compounds

o    Dictionary of Natural Products

o    Dictionary of Inorganic and Organometallic Compounds

o    Dictionary of Drugs

o    Dictionary of Analytical Reagents

COPE: Cytokines Online Pathfinder Encyclopaedia

http://www.copewithcytokines.de/

This prolific site by Prof. Dr. Horst Ibelgaufts includes a 10000+ entry online dictionary that updates The Dictionary of Cytokines and  19,000+ references on cytokines and related topics.

Glossary of Biochemistry and Molecular Biology

http://www.portlandpress.com/pp/books/online/glick/search.htm

This is a free online version of this dictionary produced by Portland Press.