Molecular Structure Practicals

Dr. Andrew C.R. Martin

Practical 1: Proteins and amino acids

An overview of proteins; starting to use RasMol; studying the amino acids
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This is a straightforward practical in which you will start to look at amino acids and their structure. If you are from a Biology background, you should be fairly familiar with the information, though you probably haven't looked at each amino acids in so much detail. If you are from a computing background, this clearly will all be new information.

The second aim of this series of practicals is to get you familiar with using the RasMol molecular graphics program. This first practical also serves to introduce RasMol and make sure that you can download and view a PDB file.

Alternative version in case there are problems with RasMol!

Practical 2: The peptide bond and secondary structure

Peptide bonds; Ramachandran plots; peptides and secondary structure
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Practical 3: Tertiary structure and molecular forces 1

Tertiary structure; disulphide bonds; hydrogen bonds; van der Waals interactions
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Practical 4: Molecular forces 2, surfaces and solvent accessibility

Electrostatic interactions; the hydrophobic effect; molecular surfaces and solvent accessibility
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Practical 5: The Protein Databank and structural classification

Using the PDB, PDBSum, MSDlite and CATH
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