World Wide Web Links

Advanced Biochemistry Fall Term, 1998

 

Directories & Search Facilities

Yahoo (Indices of everything with daily updates).
Lycos Home Page (Hunting WWW Information; Searches everything).

The World-Wide Web Virtual Library: Biochemistry, Biophysics, and Molecular Biology.
Pedro's BioMolecular Research Tools (Huge collection of WWW links).

Structure & Sequence Databases

PDB WWW Server (Protein structures in PDB format).
NDB HTTP Server (DNA and RNA structures in PDB format).
Klotho (Biochemical compounds database; view small molecules using RasMac).
National Center for Biotechnology Information (Lists many databases including GenBank).

Molecular Modeling & Graphics

Molecular Models for Biochemistry at Carnegie Mellon.
RasMol (Links to the uses of RasMol and other free molecular visualization resources).
Kinemage Files (for the Branden and Tooze book, Introduction to Protein Structure).

Journals & Societies

Protein Science  (View or download Kinemages published in this journal).
Proceedings of the National Academy of Sciences  (Browse and search the text and figures of recent issues).
Journal of Biological Chemistry  
Journal of Molecular Biology   (Abstracts in HTML; articles in PDF).
Nucleic Acids Research   (and other Oxford University Press publications).
Science  (Home Page for American Association for the Advancement of Science).
Nature   (TOC's and abstracts of current articles).
American Chemical Society (Publications Division).
American Society for Microbiology (TOC's for J. Bact. , Mol. & Cell. Biol., and others).

Miscellany & More Software Tools

Yellow BAGI (a "yellow pages" for biological software available on the Internet).
CMU Biological Sciences Front Door with links to Departmental activities.
American Universities (A directory).
BIOSCI/bionet Electronic Newsgroup Network (a set of electronic communication forums).
NIH Home Page (Activities of the outfit that pays most of the bills).

• Stuart Kushon: Database of Macromolecular Movements
  This site is rather interesting because it contains a series of movies which relates to the molecular motions of proteins. There are numerous structures in various animated file types. Pretty cool.
• Sapna Puri: Applications of Green Fluorescent Protein
  This site gives information about various projects in the scientific world which use GFP as a marker for different experiments. GFP has been used extensively to study the role of proteins, their localisation in cells, migration and transport. The site has links to laboratories who are currently working with GFP as a marker as well as work that has been done previously. It also has information about where one can obtain appropriate cloning vectors for using this protein.
• Paul Riley: All the Virology on the WWW. This website contains items of immense interest to Virologists, as well as students of Infectious Diseases in general, generated by David M. Sander, Ph.D. in the laboratory of Robert F. Garry, Ph.D. in the Department of Microbiology and Immunology at Tulane University School of Medicine. Their research centers on retroviruses, autoimmunity and retroviruses in autoimmunity. Features of the website include links to "The Big Picture Book of Viruses," online virology and microbiology courses, the "Virology Bookshop", emerging viruses, graduate programs in virology, vaccines and vaccine development, viral genome sequences, research centering on HIV and AIDS, government agencies, virology in the news, and about anything else imaginable within this very diverse field. Anyone in our class interested in learning more about virology and getting into some very serious research in infectious diseases and health should definitely look at this site. The electron micrographs and models in the "Big Picture Book" were especially fascinating.
  From the University of Washington's Health Sciences Library WWW pages, one can find almost anything having to do with health related research, a great place to start when long into subjects for a term paper or background for a research project.
• Brian Sage: Center for Genome Research
  The WWW site I found of interest was www.genome.wi.mit.edu. This is a World-Wide Web server run by the Center for Genome Research at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, USA. It contains information on map and sequence releases, software and people at the Genome Center. This site also has a very useful tool. There is a WWW program that is used to pick primers. You enter your sequence and it will tell you what are good primers to use for the PCR reaction.
• Miaomiao Wang: Metabolic Pathways of Biochemistry
  This site is an online reference of metabolism. It is designed to graphically represent all major metabolic pathways, primarily those important to human biochemistry. It has both a 2-D and 3-D vision for the processes discussed and thus can provide direct view and idea of these processes.
• Yiping Zhan: The CMS-SDSC Molecular Biology Resource
  Follow its links and you can go to almost any database and find any information that is related to biochemistry and molecular biology research on-line.
• Greg Zornetzer: RNA Secondary Structures
  This URL is the home of a database of structures for the folded (tertiary) structures of different RNA's. This may prove as a useful database if the class studies the structural features and folding of RNA molecules. RNA structures are available as postscript files, so a full PDB image does not appear to be available.

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