Biomodel: complements for learning biochemistry and molecular biology (front page image)

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Biomodel.uah.es
Material in English:

Biomodel-1: The structure of proteins and nucleic acids

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A tutorial for the structure of proteins (from amino acids to quaternary structures), nucleic acids and complexes among them. Uses 3D interactive molecular models withJSmol

Biomodel-2: Lipid bilayers and the gramicidin channel

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A presentation showing cholesterol, phosphatidyl choline, and then illustrating the assembly of a hydrated crystalline bilayer model. Then the gramicidin channel is shown in a hydrated bilayer of phosphatidyl ethanolamine. Uses 3D interactive molecular models withJSmol

Biomodel-3: Structural biochemistry for secondary school

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A self-guided tutorial, complementary to textbooks and lectures, centered on the display of 3D interactive molecular models withJSmol

Biomodel-4: DNA structure tutorial

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A 4-step tutorial of the double helix featuring molecular models withJSmol Available in English, Spanish, German, French, Portuguese, Romanian, Italian, Polish, Turkish, Chinese, Greek, Thai and Hebrew.

Amino acids structure and quiz (for smartphones)

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Designed to fit and be used in a mobile phone (touch, small screen). 3D interactive structures of the 22 amino acids and nucleobases, both as a presentation and as a quiz. Available in English, Spanish, French, Portuguese, Italian and Turkish.

Water

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Hydrogen bonds and the structure of water: structure of liquid water and ice, simulation of 10 water molecules forming a drop, all withJSmol

Virtual labs

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The Cybertory virtual laboratory allows to process DNA samples through restriction enzyme digestion and gel electrophoresis, or multiplex STR PCR and electrophoresis. Applications: sickle cell disease, celiac disease, criminal scene forensics, paternity test, pharmacogenomics of CYP450, adulteration of dairy products.

Periodic table

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with atomic, ionic and van der Waals radii, using JSmol

Stereoisomerism in biomolecules

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A collection of exercises for practicing the recognition of structure and stereoisomerism in sugars and amino acids. (Uses JSmol)

Enzymology

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Enzyme kinetics: simulations; graphical plots; fitting experimental data to Michaelis & Menten equation using nonlinear regression.

Immunology

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HIV-1 gp120 envelope glycoprotein complexed with CD4 antigen and an antibody.
(UsingJSmol; a port of the original Chime version by Richard Hunt)

Do-It-Yourself Molecules

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Draw your molecule of choice and get easily a 3D interactive model.

Articles

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A series of articles about education in Biochemistry in the University, published in the Journal of the Spanish Society of Biochemistry and Molecular Biology:

Jmol development

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A collection of contributions to documentation, tests, demo pages.

Published in Dec.2007:

more info A handbook for learning how to use Jmol in teaching, study and research, and how to develop your own tutorials with it.
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