Bioinformatics Seminars

Molecular graphics

We will use YASARA for molecular graphics applications. The first practical will start with a YASARA tutorial.

After going through the YASARA tutorial you:
Are able to read in a PDB file and to display the structure.
Are able to answer the questions in the rest of the practicals that require visual inspection.

YASARA has its own tutorial built-in, and a Yasara help document is available as a .doc file.

To get started with YASARA, play the Help movie:
  Help -->
    Play help movie -->
      Working with YASARA

And if you still think it is difficult, you can go for Hanka's YASARA course.

Make sure you are very comfortable with YASARA before you continue. You will need to use this software intensively during 3 of the 4 practicals.

The amino acids

Eventhough I believe that knowledge of all intricacies of the structure-function relation of amino acids should be part of the intellectual lugage of all biologists, chemists, etc, knowledge of the amino acids will not be part of the exam. If you want to get refreshed on the structure and function of the 20 canonical amino acids, then feel free to look at this

After completing the "Amino Acids" part (using hypothese) you will:
Be able to recognize amino acids in a 3D structure on the screen.
Be able to recognize secondary structure elements in a 3D structure on the screen.
Be able to use several advanced YASARA visualisation options.

As said, 'the amino acids' are not part of the exam, but you will learn more from the practical sessions if you spend a bit of time on the amino acids early on during the course.

Hypothase

Figure 11. Load the file HYPOTHASE.pdb in YASARA. This is obviously not a real protein, but someting we made up to make it easy for you to get used to looking at protein structures.

Find in the structure one of each:

A hydrophobic residue
A hydrophilic residue
A proline
A glutamic acid
A helix
A strand
A sheet
A core residue
A surface residue
A strand with alternating hydrophobic and hydrophilic residues

When in doubt, ask the assistant because we obviously cannot check your answers...

Question 1: Which residues form the one single helix in this molecule? What does YASARA think about this? And what do you think?

Answer

Question 2:

Figure 12. Demonstration of YASARA visualization options. Try to reconstruct this figure at your screen. Do not continue before the assistant has checked that the figures match exactly.

Answer

Supplemental material