[BiO BB] Single-domain proteins

jfreeman jfreeman at variagenics.com
Fri Oct 5 13:08:04 EDT 2001

Hi Dr. Suraj, et al.

On the bioinformatics end of things:

If a protein has two or more domains, but it is only annotated with a
single domains function, and a simple homology from that proteins domain
to another protein will give transitive false annotation assignments.

For example:

1. A--
2. A--B
3. B--C
4. C--

Given that: 1, 2, 3, and 4 are different proteins.

and domains A, B, C, and D have different functions, but you only know A
and C's functions, what you annotate protein 2 and 3 depends on what you
start with 1 or 4.  If you use simple homology to assign a function to 2
from 1, and then use this functional assignment on 2 to annotate by
simple homology protein 3, the annotation for 3 will be function A and
be completely false.

Finding single domain proteins, or important motifs, therefore becomes a
very important annotation tool.

For more information see:


Happy Hunting,

Jim Freeman

Peri Suraj wrote:
> hi group,
>   what are the advantages of single-domain proteins ?
> thanks
> SP
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