Biomodel.uah.es

Material in English:

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:

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 using Jmol or JSmol. This version should work on tablets and smartphones as well as computers with or without Java.

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 using Jmol or JSmol. This version should work on tablets and smartphones as well as computers with or without Java.

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 using Jmol or JSmol. This version should work on tablets and smartphones as well as computers with or without Java.

Biomodel-4: DNA Structure Tutorial.

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Molecular models using Jmol or JSmol. This version should work on tablets and smartphones as well as computers with or without Java. Available in English, Spanish, German, French, Portuguese, Romanian, Italian, Polish, Turkish, Chinese and Thai.

Water

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

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 21 amino acids , both as a presentation and as a quiz. Also structures of the nitrogen bases. Available in English, Spanish, French, Portuguese, Italian and Turkish.

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.
(Now usesJmol or JSmol; a port of the original Chime version by Richard Hunt)

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. Starring: sickle cell disease, celiac disease, criminal scene forensics, paternity test, CYP450 isoforms, dairy products adulteration

Do-It-Yourself Molecules

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

Get 3D structures from their name

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Get a 3D interactive model from the name or ID of the compound (small molecules).

Jmol development

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

Contact the author

Personal home page

Main home page (in Spanish)

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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