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

• 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 password.

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 Journal Search Page.  Enter the title of the journal in the window and click on the search icon.  Then look for a listing with a link to Online Access and click on it. 

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 is a table that provides this information.

Alternatively you can go to the library's One Search page, choose Articles in the pulldown menu, and copy and paste the title of the article into the search window.

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 Online Library

ACS Publications

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 Protein and Gene sequence database browsers, 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 Bioinformatics Resource Portal --home page for the Expert Protein Analysis System of the Swiss Institute of Bioinformatics with lots of useful links, including programs for analysis of both nucleic acids and proteins.
  
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• These are a few useful programs for DNA sequence analysis

   

• NEBCutter -- restriction site analysis
  
• Tm Determination -- determines the Tm of a DNA based on base composition and sequence
• WatCut -- restriction site analysis
  
• Webcutter -- a program for locating restriction sites in DNA sequence

Molecular Modeling

• Jmol -- one of the most widely used programs, relatively easy to learn, used in our CHEM 441AB
  
• Jmol Protein Explorer -- a Jmol-based program that lets you explore the structure of a protein easily
• 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
• 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 100 free programs (last updated in 2011)
  

Older software being phased out:

• RasMol -- previously one of the most commonly used programs, and possibly the easiest to learn, but not available for Mac System 10 and largely replaced by Jmol 
  
• Chime -- a Netscape "helper application" which allows you to see and manipulate images of molecules on web pages in a format similar to Rasmol, not compatible with many browsers but required to view some older web pages

• 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
• Protopedia -- type in a PDB ID and get a page with an interactive Jmol image and links to information about the protein
• NCBI Structure Group & Molecular Modeling Database (MMDB) -- these files can also be viewed in Cn3D.
• 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.  Unfortunately not updated since 1998, so many PDB structures are not listed.
  
• CATH -- another database with information about domain boundaries
  
• MakeMultimer -- gives pdb files for the native Biological Assemblies in a format that is easy to use in Jmol (e.g. each chain designated by a different letter)
• PISA (Protein Interfaces, Surfaces and Assemblies) Server -- similar to MakeMultimer
  
• NMR Representatives -- NMR structure files present an ensemble of NMR structures.  To download a file with the single most representative NMR structure, 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
• Protein Structure Prediction Center

• Database of Simulated Molecular Motions -- a collection of over 100 animations of molecular dynamics simulations of biomolecules
• DNA Animation at WEHI-TV -- truly amazing animations of replication, transcription and translation
• Virtual Cell Animation Collection -- animations on some basic biochemical processes
• Clarafi.com -- a wonderful collection of animations on biochemical and cellular processes
• ATP Synthase Animations -- animations based on the crystal structure
• More ATP Synthase Animations
• Still More ATP Synthase Animations
  
• Videos on Ribosomes from the Ramakrishnan Lab
• WW Norton Microbiology Process Animations -- great study aids!
  

Metabolism, Enzymes, and Genomes

• BRENDA, the Enzyme Database -- gives you an enormous amount of information about your favorite enzyme
• Interactive Metabolic Pathways Map
  
• Worthington Enzyme Manual
• 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
• Kegg LIGAND database -- a searchable database of enzymes and biochemical compounds

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

Jobs

Sites with information about jobs in biotechnology and related areas. 

• Biocareers.com
• Biohealthmatics.com
• Biospace Career Center
• CareerJet
• Career Profiles: Health Careers
• ChemistryJobs -- sponsored by the American Chemical Society
• GreatSampleResume.com
• HireRx
• JobHero
  
• Jobs.Net
• JobsCity.Net
• JobSearchUSA
• MedZilla
• Net-Temps
• PharmaOpportunities
• Renego
• ResumeNow
• Science Careers -- from the journal Science
• Zenopa -- pharmaceutical jobs

Societies, Organizations, and Universities

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

Vendors

• BioSupplyNet: Biomedical Research Products Source
• Biosurplus.com
  
• LABX
• MedWow
  
• Used-line.com
  

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. 
  
• 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
• Chemistry Conferences: Biochemistry -- list of upcoming conferences
• LibreTexts -- great online textbooks at undergraduate and graduate levels
• 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
• ChemSpider -- information on thousands of chemicals
• eMolecules -- searchable index properties and suppliers of chemicals