Biochemistry Links for  CSULB Students and Faculty

Students: Please explore these sites. Have fun!

Back to the Department of Chemistry and Biochemistry at California State University, Long Beach

Libraries

• COAST! -- CSULB library catalog
• CSULB Library Home Page
• Interlibrary Loan -- for requesting a copy of a journal article or book which isn't in our library
• MELVYL --University of California Libraries

Journals

CSULB students and faculty have access to full-text reprint versions of articles from a large number of journals in biochemistry and related areas.  Some sites provide public access.  Others are accessible only from campus computers, or from any computer but only for users who can provide a university ID and a CSULB PIN number.  If you don't have a library PIN, you can create one here.

NOTE: IF YOU GO DIRECTLY TO THE PUBLIC SITE FOR A JOURNAL, YOU WILL OFTEN BE DENIED ACCESS, EVEN IF CSULB SUBSCRIBES TO THE JOURNAL.  FOR THOSE JOURNALS YOU MUST USE THE FOLLOWING METHOD TO GET ACCESS:

To access an electronic version of an article, go to the library's Search Page.  Set the left-hand menu to Title/Journal Title and the right-hand menu to Journal, Periodical, Newspaper (Serial) Collection.  Enter the title or part of the title in the window and click Go.  Then look for the listing directing you to Full Text or Table of Contents Available on the Internet.  Once you get to a the site for a journal you use often, you can try bookmarking it to save time in the future (this may or may not work).

Alternatively you can go to the library's citation linker and enter the citation information to see if we have online access to a particular article.  If we have neither the online or print version, try Interlibrary Loan (above).

For the journal Biochimica et Biophysica Acta, locating a paper requires knowing which section of the journal a particular volume is in.  The BBA Decoder from UCSD is a table that provides this information.

Finally, the following services provide access to online journals to library users and may be accessed directly from campus computers or from home computers with use of a CSULB ID and library PIN number.  If you have trouble locating the link to the internet version of a journal, you can try using these web sites.

Science Direct

Wiley Interscience

ACS Web Editions

JSTOR provides access to older issues of Science, the Proceedings of the National Academy of Science, and the publications of the Royal Society of London.

DNA/RNA/Protein Sequence Analysis

• National Center for Biotechnology Information (NCBI) -- contains links to the Entrez browser and the GenBank database search, for looking up the amino acid or nucleotide sequence files for a given gene or protein, doing BLAST searches for locating sequence homologies, and various other manipulations of sequence data.

• ExPASy Molecular Biology Server --home page for the Expert Protein AnalysisSystem of the Swiss Institute of Bioinformatics with lots of useful links.
• • ExPASy Proteomics Tools -- includes links to programs for primary, secondary, and tertiary structure analysis of proteins
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• These are a few useful programs for DNA sequence analysis

   

• Cybergene Primer Design Utility -- an easy-to-use primer design program
• NEBCutter -- restriction site analysis
  
• Tm Determination -- determines the Tm of a DNA based on base composition and sequence
• WatCut -- restriction site analysis
  
• Webcutter 2.0 -- a program for locating restriction sites in DNA sequence

Molecular Modeling

• RasMol -- one of the most commonly used programs, and possibly the easiest to learn. 
  
• RasMol 2.6-UCB -- a version of RasMol which allows you to view multiple images in a single window (different molecules or different views of the same molecule)
• Chime -- a Netscape "helper application" which allows you to see and manipulate images of molecules on web pages in a format similar to Rasmol
• Jmol -- a Java application similar to Rasmol
• Protein Explorer -- a combination of RasMol and Chime, in which you can manipulate molecules both by Chime menus and Rasmol commands.  If Chime is installed as a helper, you can run this program on Netscape without downloading it.
• Cn3D -- the program developed by the National Center for Biotechnology Information.  One nice feature is that it lets you color code a protein by its domains.
  
• Mage-- the program of the Protein Society, which allows you to visualize "kinemages"
• Deep View Swiss-PdbViewer -- a versatile and sophisticated program from the Swiss Institute of Bioinformatics
• Pymol -- a program popular with protein biochemists, more sophisticated than Rasmol
• EZ-Viz -- a plugin designed to make Pymol easier to use
  
• Molsoft ICM-Browser -- a popular and versatile molecular modeling program
• Visual Molecular Dynamics (VMD) -- a visualization program favored by researchers who do molecular dynamics calculations
• Discovery Studio Visualizer -- the free version of a program produced by Accelerys
• Python Molecular Viewer (PMV) -- a program developed by the Scripps Institute
• Ballview
• Chimera -- developed by UC San Francisco
• Free Molecular Vision and Modeling Software -- a comprehensive list of over 90 free programs
  

• Protein Data Bank (PDB) -- contains structure files which can be viewed in RasMol or Chime
• First Glance in Jmol -- type in a PDB ID number and get back an interactive figure that you can display different ways and explore the contacts between amino acids or between polypeptide chains -- requires no software downloads
  
• NCBI Structure Group & Molecular Modeling Database (MMDB) -- these files can also be viewed in Cn3D.
• Molecules To Go -- another way to search the PDB
• WebMol at UCSF -- uses a Java applet called PDBViewer so that you can visualize a protein without having any software installed on your computer
• SCOP (Structural Classification of Proteins) -- an index of known protein structures arranged by structural type
• Nucleic Acid Database

• 3Dee Database of Protein Domain Definitions -- type in the PDB accession number of a protein and get a table of the domain boundaries
• CATH -- another database with information about domain boundaries
  
• Probable Quaternary Structure -- Sometimes a structure file presents only the smallest asymmetric unit, rather than the complete structure (e.g. hemoglobin files that give a dimer instead of a tetramer, DNA files thatgive only one chain).  This site generates a pdb file with the complete biological structure coordinates for viewing in RasMol or Protein Explorer.
• NMR Representatives -- NMR structure files present an ensemble of NMR structures.  To download a file with the single most representative NMR structure for viewing in Rasmol, enter the PDB ID in the window.
• FirstGlance in Jmol Snapshots Gallery -- shows how to get the most out of FirstGlance in Jmol with examples of different displays of protein structure
  
• Tutorials on How to Use RasMol and Chime
• Rasmol Reference Manual
• Select Commands in Chime and RasMol -- how to formulate commands to select atoms or groups of atoms
• Cn3D Tutorial

Metabolism, Enzymes, and Genomes

• BRENDA, the Enzyme Database -- gives you an enormous amount of information about your favorite enzyme
• Metabolic Pathways Chart (PDF format chart from Sigma Chemical Company, suitable for framing)
• Worthington Enzyme Manual
• Biobar -- "a tool for browsing biological data and databases"
  
• Biocyc -- a collection of 260 pathway/genome databaases
  
• ENZYME, the ExPASy enzyme nomenclature database
• ExPASy Biochemical Pathways -- type in a keyword and get link to a location on the Biochemical Pathways chart of Boehringer-Mannheim
• KEGG -- Kyoto Encyclopedia of Genes and Genomes
• LIGAND database -- a searchable database of enzymes and biochemical compounds
• Metabolic Pathways of Biochemistry -- an educational site on metabolic pathways
• PUMA -- evolutionary analysis of metabolism
  

Methods and Protocols

These sites are for looking up protocols for many procedures in biochemistry and molecular biology.

• Protocol Online
• Cell and Molecular Biology Online
• Molecular Station
• Molecular Biology Protocols
• PrimerDesign.com
  
• PCRLinks.com
  

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  A link to the facility at San Diego State University which provides oligonucleotide synthesis and DNA sequencing for CSU faculty and students.

   

• CSUPERB Microchemical Core Facility Homepage

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Jobs

Sites with information about jobs in biotechnology and related areas. 

• Bio.Com Jobs
• Biohealthmatics.com
  
• Biospace Career Center
• CareerJet
  
• ChemJobs -- sponsored by the American Chemical Society
• CSUPERB Job Links -- a page of job-related links from the CSU Program for Education and Research in Biotechnology
• HireBio
• HireHealth
• HireRx
• HotJobs
• +Jobs America
• +Jobs California
• Jobs.Net
• JobsCity.Net
  
• MedZilla
• Monstertrak
• Net-Temps
• PharmaOpportunities
  
• Science Careers -- from the journal Science
• ScienceJobs
• SciWeb Biotechnology Career Center
• Snaill

Societies, Organizations, and Universities

• FASEB Member Directory
• American Society for Cell Biology
• American Society for Biochemistry and Molecular Biology
• CellMolBiol Online - Societies and Organizations
• National Science Foundation

Vendors

• BestLabDeals.com
• BioSupplyNet: Biomedical Research Products Source
• Biosurplus.com
  
• LABX
• SciQuest

Other Lists of Biochem/MolBiol Sites

• Art's Biotech Resource -- a huge collection of links to just about everything
• Allyn's websites
• Cell and Molecular Biology Online
• CSULB Library: Research by Subject - Chemistry/Biochemistry
• CSULB Library: Research by Subject -- Biological Sciences
  
• Harvard Molecular and Cellular Biology Department Biology Links
• Pedro's BioMolecular Research Tools -- a very extensive list of links, used to be the best site of its kind but has not been updated since 1996
• Voet/Voet/Pratt: World Wide Web Links

Biochemistry Songs

• The Biochemists' Songbook MP3 Files -- recordings of biochemistry songs written by Dr. Harold Baum of the University of London
• Kevin Ahern's Wildly Popular Metabolic Melodies -- from a professor at Oregon State University
  
• Musical Chemistry -- from Amy Hartnell of Britain
• Beta-blocker Blues and Other Blues for the Lecture Theater -- from the University of Kuopio in Finland.  Note: The authors published a paper demonstrating that listening to the songs improved student test scores!
• Transcription, The Music of Protein Sequences -- music based on amino acid sequences (one of many such sites, Google "protein music" for lots more)
  
• Jeff Cohlberg's Biochemistry Songs -- last but not least
  

Other Biochemistry Sites

• Biophysical Society Educational Resources
  
• Instructional Biochemistry at UCSB -- an online course which makes extensive use of molecular modeling images
• Indiana State University Medical Biochemistry page -- great summaries of essential concepts in biochemistry
• Chemfinder.Com -- information on thousands of chemicals
• eMolecules -- searchable index properties and suppliers of chemicals
• Properties of Detergents
• DNA Animation at WEHI-TV -- truly amazing animations of replication, transcription and translation
• Virtual Cell Animation Collection -- animations on some basic biochemical processes
  

• Grad School Tips -- general information about graduate school
• Hoaxbusters -- If someone just sent you a warning about a new virus, check this site to see if it's real or a hoax.
• ScholarshipHelp.org
  
• USNO Master Clock Time