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Jmol displays of 3-D structures of Biological molecules

Update available! Click here to go to safer Jsmol version

Bad news and Good news!


This section of the BioTopics website relates to Biological chemicals, allowing them to be visualised as 3-D interactive molecular images which can be explained in an interactive way.

These pages depend on Java (not to be confused with javascript) which extends the display capability and interactiveness in a flexible way. Unfortunately, Java has recently been found to suffer from various security weaknesses, the result of which is that most browsers filter pages that use Java, and only proceed after prompts and warnings. Apart from being inconvenient and alarming to users, it sometimes disturbs the flow of data, affecting page functioning. If you opt to follow the links in the table below you are likely to be repeatedly warned about security issues. I believe there is no specific risk in the files themselves - they are not virus-infected - but accessing them via Java may open users' computers to malicious functions. These pages are all easily accessible after passing the warning page which is shown at first.

However most of these features can be replicated using a minor modification involving javascript: JSMOL - which is not a security risk. Work will shortly commence on converting all this material (and more!) to this format which is compatible with most computers and tablets, as long as javascript is enabled in their browsers!

I have now produced a series of JSMOL pages as a replacement to these ones. Here is the equivalent menu page: JSmol menu

Java security work-around

You can now add:
http://www.biotopics.co.uk/JmolApplet/
to your exception site list (cut and paste the line above).

This can be accessed from Windows control panel, search for Java, double click Java icon to get to Java control panel, then security tab and edit site list ...

Please let me know if this is successful, or if you need more assistance.
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.

Most Apple desktop and laptop models use Java and should give very clear images with these files - especially the proteins on larger screen sizes.
Sadly, iPads and most tablets do not use Java, so these molecules will not display on them.

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
starch-iodine test amylose-iodide complex
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
DIPEPTIDE
Special request Leucine-alanine
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 proteinsCollagen
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  
nucleotidesAMP,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
ChlorophyllAcetyl choline Artificial sweeteners
Paracetamol Opiates and cannabinoids Salicin and Aspirin
Capsaicin
ANTIBIOTICS
Beta Lactams Examples Other categories
of antibiotic
Examples
Penicillins
(Penems)
 Penicillin G 
 Amoxicillin 
 Ampicillin 
 Methicillin 
Macrolides  Erythromycin 
Cephalosporins
(Cephems)
 Cephalexin  Tetracyclines  Lymecycline 
Monolactams  Aztreonam  Quinolones  Ciprofloxacin 
Carbapenems  Meropenem  Aminoglycosides  Streptomycin 
Beta-lactamase inhibitors Clavulanic acid Sulfonamides  Sulfamethoxazole 
Diaminopyrimidine Trimethoprim
Glycopeptide Vancomycin
Oxazolidinone Linezolid
[missed out - a number of images of vitamins]

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.

And the I find the Jmol application modelkit very helpful in modifying and fine-tuning molecular structures. Several files here need this treatment.

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.

The DrugBank database is a unique bioinformatics and cheminformatics resource which I have found quite useful.
ChemSpider is a free chemical structure database owned by the Royal Society of Chemistry.

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. Here is a very useful molecule viewer he has put together.

(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/

Dr 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."

Orientations of Proteins in Membranes (OPM) database
OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer.
This is quite a comprehensive selection of important biological molecules, visualised as a sandwich between two discs of red and blue dots, showing how these proteins interact with membranes on the surface of, or within, the cell.

Please let me know of any other Jmol based information sources at an appropriate level.




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