Dear Jacob,
I have developed a structural conservation function in MANORAA.org that acts by
using ligand's rigid fragment as a probe to see what protein's active site
residues retain its position relative to the ligand in gradient colours.
For example, with staurosporine as a query molecule.
h
I am also not sure of what your goal is, but you can build a sequence profile
for your sequence and use that profile as input instead of your sequence. You
can do this by aligning a set of sequences homologous to your target sequence,
and use that alignment as input for, for example, HMMER or HH
Not sure if I understand the question right, but wouldn't phi-blast do
trick. You supply on too your conserved pattern and blast again.
Christian
Am 20.12.2017 19:37 schrieb "Keller, Jacob" :
> Dear Crystallographer-Bioinformaticians,
>
>
>
> Is anyone aware of a way to tweak BLAST or similar so
Dear Crystallographer-Bioinformaticians,
Is anyone aware of a way to tweak BLAST or similar software to be able to
specify certain residues to be absolutely required, e.g., active site residues?
I guess one can winnow broad-scale resuts with scripts, but it would seem to be
a pretty common type
