149

Task 11.13

Example:

Visualize and model the inhibition of HIV-1 protease with indinavir (PDB ID: 1HSG)

in PyMOL (please download PyMOL [https://www.pymol.org/] and the sequences from

PDB [https://www.rcsb.org/pdb/home/home.do] beforehand). Answer the following

questions:

• How to bring together the complex of protease and ligand?

• How are the charges distributed at the point of contact?

• Where is the catalytic center? What holds the center together?

Task 11.14

How can we bioinformatically predict the localization of a protein?

Task 11.15

Describe how to bioinformatically screen a protein for its localization (e.g. membrane

protein, transcription factor) in eukaryotes/prokaryotes (name software/database and

briefly describe).

Task 11.16

Describe what is meant by neural (machine) learning. Are there any differences between

this and human learning?

Task 11.17

Name databases/software where you can get information on signal peptides (e.g. sequence

or localization).

Task 11.18

Develop a simple program that examines a sequence for its localization. Also enumerate

what parts this program would consist of.

Task 11.19

Cellular communication can also be viewed informatically. Briefly explain how to calcu­

late the information content of a message and show an example.

Task 11.20

Biological communication has problems with the transmission of information, what? How

are these problems solved biologically by the cell (explain with an example)?

11.3  Exercises for Chap. 11