148

Task 11.5

Name databases/software where they can find information on proteins.

Task 11.6

Name software they can use to visualize and analyze protein structures and interactions.

Task 11.7

What can be found in the SCOP and CATH databases? What are the similarities and

differences?

Task 11.8

To get a conclusion about the possible function, it is helpful to examine a protein sequence

for specific protein domains and sequence motifs. How can the function of a protein

sequence that has not yet been assigned a function from experiments be investigated using

different software or database queries? In doing so, highlight differences between the

programs.

Task 11.9

Name and describe databases/software that can be used to screen a protein sequence for

conserved regions/domains.

Task 11.10

Describe how to identify conserved motifs using multiple alignment.

Task 11.11

You have ten different sequences and want to examine them for conserved sequence

regions. Name databases/software that you can use to perform such a multiple alignment.

Task 11.12

Example:

Now download the protein sequence for the “TAR protein” and perform a search with

the PROSITE database (https://prosite.expasy.org/) and the AnDom software (https://

andom.bioapps.biozentrum.uni-­wuerzburg.de/index_new.html) in the next step.

Which of the following statements are correct (multiple answers possible)?

A. Both programs find a double stranded RNA-binding domain (dsRBD).

B. Neither program finds a match for a protein domain.

C. AnDom performs a structural analysis based on the SCOP classification.

D. Based on the dsRBD domain I found, I can assume that my protein binds to double-­

stranded RNA molecules.

11  Design Principles of a Cell