If you do not see a revolving display of the letters JMOL below, you may need to click here to
Download Java Jmol displays of 3-D structures of Biological molecules
These files have been written or converted to use the Jmol Java applet (currently version 11.00 on this server), so they ought to be visible in almost all modern computers.
However Internet Explorer 6 with Windows XP (and also IE7 with or without Windows Vista) may block this functionality; images may need to be clicked on before they become movable using the mouse. Some of the control scripts may also trigger an over-cautious reaction.
Please use the feedback link on the left to let me know if these images do (or do not) display on your computer.
The three-dimensional, rotatable, scalable images on these pages should be fairly easily displayed using the Jmol Java applet, if you have Java enabled in your browser.
Jmol, which is open source (free), runs from the same server as these
pages and so is available to all users (effectively regardless of
browser type).
It is an alternative to the Chime plug-in, which users
have to install on their own computer (not easy with educational
networks). Unlike Chime, Jmol is also being continuously developed.
Although there will be an initial delay as the applet loads, subsequent
pages should be quicker. Each link below will bring in a separate
overlay page, leaving this list page beneath it. After use, simply
close these windows in the usual way (use the icon below or click on
the X in the corner of the browser window).
| CARBOHYDRATES |
| Monosaccharides |
| hexoses |
glucose |
alpha and beta glucose |
| fructose |
glucose-galactose comparison |
| pentoses |
ribose |
deoxyribose |
| glucose derivatives |
glucosamine |
N acetylglucosamine |
| Disaccharides |
| glucose dimers |
maltose |
cellobiose |
| mixed dimers |
sucrose |
lactose |
| Polysaccharides |
| storage compounds - animal |
glycogen |
. |
| storage compounds - plants |
amylose [another form of amylose] |
amylopectin |
| structural compounds - plants |
cellulose |
|
| AMINO ACIDS |
| All shown on one page |
20 amino acids |
Individual amino acids
- seen a little larger |
glycine,
alanine,
valine,
leucine,
isoleucine,
serine,
threonine,
lysine,
histidine,
arginine,
phenylalanine,
tyrosine,
tryptophan,
cysteine,
methionine,
aspartic acid,
asparagine,
glutamic acid,
glutamine,
proline |
| PROTEINS |
| Levels of protein structure |
General principles
| as shown by Insulin |
| as shown by Haemoglobin |
as shown by Myoglobin |
| Enzyme structure |
Amylase as an example
Pepsin
Pepsinogen
|
More to be added soon |
| Fibrous proteins | Collagen | |
| LIPIDS (FATS and OILS) |
| Sub-units |
glycerol |
saturated and unsaturated fatty acids |
| Polyunsaturated fatty acids |
alpha-linolenic acid
| gamma-linolenic acid |
| More about functional foods |
plant sterols and stanols and their esters
| |
| Neutral fats |
triglycerides |
monoglycerides and diglycerides |
| |
phospholipids |
phospholipid bilayer |
| Sterols and steroids |
cholesterol |
More to follow |
| NUCLEIC ACIDS |
| Section |
DNA - see also * below |
|
| nucleotides | AMP,TMP pair |
GMP,CMP pair |
| bases |
DNA bases |
RNA bases |
| co-enzymes |
ATP |
NAD and reduced NAD |
| Other molecules of biological interest |
| Caffeine |
Penicillin |
Another fungal product |
| Antimalarial compounds |
Taxol |
Anti-Tuberculosis Drugs |
| Chlorophyll | Acetyl choline |
Artificial sweeteners |
| Paracetamol |
Opiates and cannabinoids |
Salicin and Aspirin |
I am very grateful to the (largely unknown) people who provided the original data files for these molecules, mostly in
.mol , .pdb and .xyz format.
However not all of the representations of molecules on the internet are completely reliable, so beware.
I have recently started producing my own co-ordinate files (or modified/corrected versions of other people's files!) using ACD
ChemSketch.
You can access lots of information from the
RSCB Protein Data Bank which "provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease". It has a very readable section Molecule of the Month - Alphabetical List which gives background information about Biochemical molecules without going overboard with (much) excessive detail or heavy graphics.
The
European Bioinformatics Institute is an Outstation of the European Molecular Biology Laboratory and provides access to all sorts of information about biological molecules.
RASMOL is a stand-alone 3D viewer for molecules using these formats,
effectively an application on which Chime, Protein Explorer and Jmol
are based
*RasMol homepage
*RasMol for RISC OS
There is also a stand-alone application version of Jmol which is also
available for development work, independent of web page format. This is especially good in full screen mode.
*Jmol overview
Jmol-based molecular visualisation files on other web sites
Jmol is looked after by a very enthusiatic (worldwide) team of practitioners:
I am extremely grateful to Eric Martz,
Professor Emeritus, University of Massachusetts, who advised me to concentrate on the use of Jmol for molecular display on these web pages rather than waste time with Chime. His current interest is "Macromolecular Visualization and Structural Bioinformatics"! and is involved in FirstGlance in Jmol and Protein Explorer, both of which are used in exploration of protein structure.
My sincere thanks also go to Bob Hanson, Professor of Chemistry at St. Olaf College Northfield, MN, USA, who maintains and extends Jmol -see the Jmol development page. He appears to fix bugs as fast as they are discovered, and add new features at an impressive pace.
(Webmasters only: Jmol can be downoaded here:
http://jmol.sourceforge.net/download/
)
Dr Angel Herráez, Univ. de Alcalá (Spain) is another enthusiastic user of Jmol (he has just produced a book to explain its use - more details later).
He maintains some very useful resources such as:
*DNA structure a modified version of an excellent Chime-based tutorial
*Molecular Models for secondary education an impressive tutorial translated from Spanish
Both can be accessed from an index page at
http://biomodel.uah.es/en/
Frieda Reichsman has also produced an excellent range of molecular animations visible online at http://www.moleculesinmotion.com/
Proteopedia is a collaborative, 3D encyclopedia of proteins and other molecules. Eric Martz says "Proteopedia will develop into one of the most useful on-line reference sites for
structural information about macromolecules. Proteopedia already
contains an automatically-generated page for each of the nearly
50,000 entries in the Protein Data Bank. This automatic page contains
the molecule in Jmol, with green links to display every site and
ligand in the PDB file (echoing their full names), the abstract of
the paper, and links to a few other particularly useful structure
services and resources.
Students and Educators can develop macromolecular structure tutorials
in Proteopedia far more easily than in any other system at present."
Please let me know of any other Jmol based information sources at an appropriate level.