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- There are various ways to obtain certain types of information about a
protein. The method(s) and database(s) that you will want to use will
depend a great deal on what kind of information you want.
- Databases such as Swiss-Prot
can be used to obtain the primary structures (amino acid sequences) of
proteins. As with nucleic acids, there are two basic methods for
searching sequence databases: (1) particular keyword label (e.g.,
"cytochrome c"). PIR in particular
allows a variety of different types of keyword characteristics to be
searched; or (2) search engines can be used to hunt for sequences that
are similar to one another. As an analogy, you could search a phonebook
for a number (sequence) associated with a particular name (protein), or
you could search a phonebook to determine the names of all the people who
had phone number ending in 7675.
- Databases such as Blocks or
Prodom provide
information about sequence and structural patterns in proteins. These
databases group proteins that contain similar active sites or
substructures, and thus differ from search engines that blindly compare
all primary sequences. They are particularly useful because the
structure of a protein will determine its function, yet there are no
good ways to compare overall structure. As an analogy, if you wanted to
know who was related to who in a town, it might be easier to look at
last names in a phonebook rather than pictures in a yearbook.
- Databases such as NRL-3D and
Entrez contain
information about the overall three-dimensional structures of proteins.
As an analogy, if you looked up a name in the phonebook, this would be
the yearbook that would show his or her picture.