Molecular Structure Practicals

Dr. Andrew C.R. Martin

Practical 1: Proteins and amino acids (Wed 30 September 2009)

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 (Mon 5 October 2009)

Peptide bonds; Ramachandran plots; peptides and secondary structure
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Practical 3: Tertiary structure and molecular forces 1 (Wed 7 October 2009)

Tertiary structure; disulphide bonds; hydrogen bonds; van der Waals interactions
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Practical 4: Molecular forces 2, surfaces and solvent accessibility (Mon 12 October 2009)

NOTE STARTS AT 4pm

Electrostatic interactions; the hydrophobic effect; molecular surfaces and solvent accessibility
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Practical 5: The Protein Databank and structural classification (Wed 14 October 2009)

Using the PDB, PDBSum, MSDlite and CATH
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