Below are four different molecules. The first one (A) shows the ligand from the animation, the other drawings (B, C and D) represent the version 1, 2 and 3 of our antidote. For every version, there is a 3D structure modelled in Yasara.
Look at the different drawings of antidotes. Mark the atoms that may be involved in interactions with the protein. Answer
Study the different models of the antidote in Yasara.
To make it easier, we have already created scenes in Yasara so that you can quickly see the differences. Open the scenes by clicking File > Load > Complete scene. Choose ligand_version1.sce. This opens a ball-and-stick representation of the ligand. The venom is shown as a cartoon, and the amino acids close to the ligand are shown as sticks.
After looking at ligand_version1.sce, look at ligand_version2.sce and ligand_version3.sce.
Which ligand would you use as an antidote? Explain why. Answer
You have reached the end of this practicum, hopefully with the right
antidote. That one is really used to treat rattle snake bites. So,
in this case bioinformatics was used to help solve a medical
problem. However, sometimes all we can do is try to understand how a
disease works. The Retinitis Pigmentosa practicum gives you a nice
example of such a situation.
If you liked working in Yasara, look in the section More in 3D. You will learn how to make nice pictures in Yasara for reports and
science projects.
