MRS to search for a database entries of which you know the name, or some text
that they contain. MRS can search in 50-100 databases and works a bit like
Google, but since MRS knows what it is looking in, in can search much
smarter than Google. So, you search with one or a few keywords.
BLAST searches for homologs in sequence and structure database (i.e. in SwissProt,
the PDB, EMBL, etc). So, you search with a (part of a) sequence.
CLUSTAL can be used to align (multiple) sequences. BLAST also makes alignments,
but the BLAST alignments are only pairwise, and are only of a part of the
proteins. With CLUSTAL you can align whole sequences and more than two of them.
YASARA is a visualiser (and much more; but for our course only a visualiser) for
macromolecular structures.