This is a homepage for:

Dr. James K. Zimmerman, Emeritus Professor  163 Jordan Hall  864-656-3593 JKZMM@Clemson.edu

Sites that might prove useful

Biochem4schools An absolutely wonderful site run by The Biochemical Society (UK).  Over 200 resources keyed for levels of understanding from middle school on up.  Has structures, tutorials, and is a wonderful resource.

Proteopedia--A fantastic collection of 3D information for protein and biomolecular structures.  Introduced in 2010 and is still building.  This can be added to and edited by viewers.

An approach to learning Biochemistry by William Anderson at the University of New Mexico.  Very insightful site.

MIT course materials--you have to scroll down a bit from the opening to get to the list of courses

    Biology index (includes biochemistry [chemical biology]
    Chemistry index

World Index of BioMolecular Resources in Chime.

An absolutely fantastic place to explore if you want information on almost any molecular structure. These are collections of tutorials from around the world. There are tutorials on ribosomes, zinc fingers, metabolic cycles, and about anything else you can imagine. I find it difficult to navigate, but the site is great. A very comprehensive site that has many, many links. If you want to find something on electronic search sites, molecular modeling, protocols, etc., this would be an excellent place to start. It is housed at the California State University at Long Beach. It is maintained by Dr. Jeffrey Cohlberg. This program requires you have CHIME on your computer.  CHIME is free and can be downloaded by visiting www.mdlchime.com and following instructions

Some Representations of Small Molecules

Complement Structures

This is just an interest of mine. It includes all of the X-ray structures of complement proteins I can find plus some NMR structures.  Many of the JPEG figures are very fuzzy, but are there to help with some idea of structures or organization. To see the pdb (3D figures), click on the appropriate boxes with an x.

Molecular Structures

Run out of Okanagan University College in British Columbia, Canada.

Structures of Biologically Active Materials

Information on all kinds of pharmaceuticals, including structures (not CHIME). Run by the bioinformatics people at the Institute for Chemistry and Cell Biology at the Harvard Medical School.

The Online Macromolecular Museum

Fantastic site. Does require Chime, but that is free and can be downloaded from this site. Contains tutorials on various proteins using rotating 3-D models. Tutorials are very informative.

Dictionaries

Merck Manual of Diagnosis and Therapy The 17th edition of the Merck Manual of Diagnosis and Therapy (1999). Very good for Nutritional Disorders, Endocrine.Metabolic Disorders, and others.
Medical Dictionary No attribution on the home page but is run by Chris Endres. Good medical dictionary. More than 20,000 terms.  I found it easier to use the alphabetical listing rather than the Google search.
Dictionary of BioTech life science terms From the University of Texas and Indiana University
Dictionary of Science and Technology Put out by Harcourt. Can do overall searches or search within fields.
Dictionary of Genomics Terms Put out by the Cambridge Healthtech Institute (CHI) based in Massachusetts. Good search engine covering a wide range of fields.
Dictionary of Chemical Terms Put out by the International Union of Pure and Applied Chemistry (IUPAC). An online version of their "Gold Book" of officially approved terms. More than 7000 entries.
Medical & Pharmaceutical Directory Very good for acronyms. Run by Pharma-Lexicon LTD of Hastings, United Kingdom. More than 40,000 terms.
An on-line medical dictionary run by Dr. Graham Clark at the Dept. of Medical Oncology, University of Newcastle upon Tyne.
Cytokine Encyclopedia A very comprehensive compilation of links and definitions concerning cytokines.
Dictionary of Units of Measurements From the University of North Carolina. This site allows one to locate definitions of units and usually gives pretty good conversions. A very useful site.

Other Dictionaries
          Merriam Webster
          Lexico

Protocols

Protocols of all types

A wonderful collection of protocols of all types for RNA, DNA, and protein procedures. It also contains many molecular biology and microbiology protocols. It is run by Dr. Longchen Li, a postdoc at UCSF. I highly recommend the site.

More Protocols

A site run by Bio Online. I think more difficult to follow than the list above, but includes different areas.

Polymerase Chain Reaction Tools

Collection of sites explaining PCR with all kinds of variants, such as AFLP, inverse PCR and many others.  Excellent collection.  This site is run by Silvio Jesús Krivokapich.

Very nice explanations of biochemical and molecular biological procedures by M.A. Campbell at Davidson College, NC.

Data Bases

National Center for Biotechnology Information

Good site for BLAST, FASTA, and many other search and background sites in biochemistry

Protein Information Resource

Run by the National Biomedical Research Foundation at Georgetown University. Can search for sequence data, properties, PubMed links, and other information about just about any protein. Lots of good information.

Worthington Enzyme Manual

Lots of good information about a lot of enzymes. Also has a lot of molecular and cell biology listings. A commercial site that also pushes their products.

Enzyme Data Base

Called BRENDA and run by the Institute of Biochemistry at the University of Cologne. Lists data on over 3500 enzymes such as pH optima, temperature optima, how to store the samples, EC numbers, common names, etc. Can be searched in a variety of different ways. Terrific site.

Prolysis

French site with many links to information about proteases and their inhibitors. A lot of good 3-D information as well as tables of inhibitors.

MEROPS

A comprehensive list of proteases and their inhibitors.  Fantastic site.  Gives links to 3D structures as well.  Run by a small team headed by Neil D. Rawlings and Alan J. Barrett and funded by  financial support from the Medical Research Council of the UK, and the Wellcome Trust.

The Mammalian Degradome Database

Another protease site, this one run by the Department of Biochemistry and Molecular Biology from the Universidad de Oviedo, and  the Instituto Universitario de Oncologia del Principado de Asturias (IUOPA) in Spain headed by Dr. Carlos Lopez-Otin.  It includes a very nice page of human diseases tied to proteolytic enzymes.

Web notebook for chemicals

Good source for specific information on almost any chemical.  Done by NIST!

Database of 21 million chemical structures with links to journal articles.  A free service of the British Royal Society.

A site that takes PDB files and converts them to the most probable quaternary structure.  It will not be updated after August 2009 and will be discontinued later, but right now is very useful when one wants a quaternary structure and only the monomer structure is given in the pdb files.

A site that calculates lots of protein parameters, including A₂₈₀, based on amino acid content.  It does require an accession number from ExPASy.

Metabolic Pathways

There are many good websites for metabolic maps.  A few connections are given below

MiniMaps.  Housed by the IUBMB and done by Dr. Don Nicholson

AniMaps.   Housed by the IUBMB and done by Dr. Don Nicholson.  Requires Flash.

A general overview of metabolism by Dr. Pedro Silva

Glycolytic Pathway From the University of Texas. Has information on reactions, enzymes, structures, kinetics, and a quiz.

A site from Karl J. Miller labeled the Metabolic Pathways of Biochemistry. Fantastic site. Great pathways. Has Chime structures on substrates, coenzymes, etc. Really nice.

 

A site from Joyce Diwan and Scott Bello of Rensselaer Polytechnic Institute.  Fairly complete.  Does ask for students to have CHIME.  Should skip to the bottom and click on the icon for metabolic pathways on the left.

 

A site from Dr. Jim Hardy from the chemistry department at the University of Akron.

ExPASy.  Run by the Swiss Institute of Bioinformatics

A very interesting site run by Dr. Mathijs Doets at Erasmus University, Rotterdam.  It has animation of the metabolic interplay between various organs and the metabolic cycles from the newly fed state to starvation.  This is done at several different levels starting with an overall view, going to individual organs, and then to individual organelles.  Requires Shockwave.

A site produced by North Dakota State University in Fargo, ND has several movies that are interesting.  Despite being labeled as "first look" and "advanced look", the explanations are at a beginning level, but quite useful.  The movies are

ATP synthase
Electron transport chain
Mitochondrian protein transport
Transcription
mRNA processing
mRNA splicing
Translation
Lac operon

Very nice animation of the ATP synthase molecule.  Done by Don Nicholson.  Sponsored by the IUBMB.  Requires Flash.

Conversion of Units

Dictionary of Units of Measurements

From the University of North Carolina. This site allows one to locate definitions of units and usually gives pretty good conversions. A very useful site.

From OnlineConversion.com

Allows one to convert one set of units to another easily. Also has a "Fun Site" with some unusual information.

Quick conversions of units

A very nice site run by Dr. Christophe Berthold at the University of Geneva.

Membrane Protein Pages

A very good collection of membrane channel structures with details.  Maintained by Dr. William McClure at Carnegie Mellon University.  Requires CHIME.

A Membrane Protein Data Bank.  Run by Dr. Martin Caffrey of Ohio State University.  Ties directly with the Protein Data Bank and is updated weekly.  One can find a protein by name or PDB identifier or one can look through the extensive list of membrane proteins listed and make a choice from there.  Lots of good information on each entry.

Another Membrane Protein Data Bank.  Run by Stephen White at UC Irving.  Very extensive listing of crystal structures of membrane proteins.  Has them neatly categorized.  Gives the resolution, the PDB code, links to the image, links to the coordinate file, and links to the paper via PubMed.  Very nice. Requires CHIME.

Lab Simulations

A wonderful exercise on protein purifications.  It was created and is maintained by the School of Biochemistry and Molecular Biology at the University of Leeds, Dr. A.G. Booth

A virtual biochemistry laboratory.  A site from the Nobel Institute.  It requires Shockwave Player 8 (a free down-load).  Based on a video game.  Rather crude and at a low level, but interesting.  It takes a while to get used to their conventions.