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3-D interactive structures of Biological molecules

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CARBOHYDRATES - in Jsmol format
hexoses glucose alpha and beta glucose
fructose glucose-galactose comparison
pentoses ribose deoxyribose
glucose derivatives glucosamine N acetyl glucosamine
glucose dimers maltose cellobiose
mixed dimers sucrose lactose
fructo-oligosaccharides nystose inulin
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 - in Jsmol format
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
Special request Leucine-alanine
PROTEINS- in Jsmol format
Levels of protein structure General principles as shown by Insulin
as shown by Glucagon, Fibroin as shown by hCG
as shown by Haemoglobin as shown by Myoglobin
Enzyme structure Amylase as an example
More to be added soon
Fibrous proteinsCollagen
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 
Section DNA  
nucleotidesAMP, TMP pair GMP, CMP pair
bases DNA bases RNA bases
co-enzymes ATP NAD and reduced NAD
Nucleoside analogues Emtricitabine
Fialuridine XXX
Non-nucleoside reverse transcriptase inhibitor ( NNRTI) Efavirenz
Base analogues 5-FluoroUracil (5FU)
Nucleotide analogues Remdesivir
VITAMINS - in Jsmol format
Fat Soluble Vitamin A Water Soluble Vitamin B1
Retinal Vitamin B2
Vitamin B3
Vitamin D Vitamin B5
Vitamin B6
Vitamin E Vitamin B7
Vitamin B9
Vitamin K Vitamin B12
Vitamin C
ANTIBIOTICS - in Jsmol format
 Penicillin G 


Beta-lactamase inhibitors

 Clavulanic acid
Other categories
of antibiotic
Macrolides  Erythromycin 
Tetracyclines  Lymecycline 
Quinolones  Ciprofloxacin 
Aminoglycosides  Streptomycin 
Sulfonamides  Sulfamethoxazole 
Diaminopyrimidine  Trimethoprim
Glycopeptide  Vancomycin
Oxazolidinone  Linezolid
Lipopeptide Daptomycin
Depsipeptide Teixobactin
Cyclic peptide Lugdunin
2-Amino-1,3,4-thiadiazole Halicin

Other molecules of biological interest
Blank Canvas Caffeine A fungal product
Antimalarial compounds Taxol  Anti-Tuberculosis Drugs
Chlorophyll Artificial sweeteners Stevioside
Paracetamol Opiates, opioids and cannabinoids Oxycodone (OxyContin)
Salicin and Aspirin Capsaicin Salbutamol, terbutamine, adrenaline and triamcinolone
Acetyl choline AZT 5FU
Water molecule Hydrogen bonds in water Water - moving molecules Structure of ice

More molecules to be added in the near future
Please get in touch with any suggestions for candidate compounds (or categories)

Web references and useful websites

The Protein Data Bank (PDB; https://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules, now containing more than 100,000 structures.

Structural View of Biology is a portion of the PDB, focusing on the biological function of the molecules.

Orientations of Proteins in Membranes (OPM) database "provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer."

FirstGlance in Jmol is a simple tool for macromolecular visualization.

ChemInteractive is a free site designed to promote active learning of Chemistry. It is targeted at students learning Organic Chemistry in the early years of College or University programmes.

The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

ChemSpider is a free chemical structure database owned by the Royal Society of Chemistry.

Jmol/JSmol interactive scripting documentation

An Introduction to Jmol* Scripting Nathan Silva and David Marcey

Possibly relevant
material available online
(from Amazon.com)

Possibly relevant
material available online
(from Amazon.co.uk)

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