Re: [ccp4bb] Finding Homologs with Specific Residues Conserved

[Duangrudee Tanramluk]

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. 
http://mahori.icbs.mahidol.ac.th/Manoraa/sstq/ligandquery.php?queryby=lig=STU

You can input the atoms of the ligand that you want to use for 
superpositioning. It will browse through the whole protein databank to find the 
PDB structure to find all the binding partners and often including their 
structural homologs. Is that what you are trying to do?

Sincerely,
Duangrudee Tanramluk

---
Duangrudee Tanramluk, Ph.D.
Institute of Molecular Biosciences, Mahidol University
Puttamonthon 4 Rd., Salaya, Nakhon Pathom 73170 THAILAND
http://manoraa.org

Re: [ccp4bb] Finding Homologs with Specific Residues Conserved

[Joana Pereira]

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 HHPred. You can also 
let HMMER or HHPred build these profiles for you by giving your sequence as 
input and play with the parameters.

Best,

Dr. Joana Pereira
--
Postdoctoral Researcher
Department of Protein Evolution

Max Planck Institute for Developmental Biology
Spemannstraße 35
72076 Tübingen
GERMANY

> On 20 Dec 2017, at 18:35, Keller, Jacob  wrote:
> 
> 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 of thing to do, and might change 
> results slightly a la psi-BLAST.
>  
> All the best,
>  
> Jacob Keller
>  
> +
> Jacob Pearson Keller
> Research Scientist / Looger Lab
> HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> (571)209-4000 x3159
> +
>  
> The content of this email is confidential and intended for the recipient 
> specified in message only. It is strictly forbidden to share any part of this 
> message with any third party, without a written consent of the sender. If you 
> received this message by mistake, please reply to this message and follow 
> with its deletion, so that we can ensure such a mistake does not occur in the 
> future.

Re: [ccp4bb] Finding Homologs with Specific Residues Conserved

[Christian Roth]

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 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 of thing to do, and might change
> results slightly a la psi-BLAST.
>
>
>
> All the best,
>
>
>
> Jacob Keller
>
>
>
> +
>
> Jacob Pearson Keller
>
> Research Scientist / Looger Lab
>
> HHMI Janelia Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
> 
>
> (571)209-4000 x3159 <(571)%20209-4000>
>
> +
>
>
>
> The content of this email is confidential and intended for the recipient
> specified in message only. It is strictly forbidden to share any part of
> this message with any third party, without a written consent of the sender.
> If you received this message by mistake, please reply to this message and
> follow with its deletion, so that we can ensure such a mistake does not
> occur in the future.
>
>
>

[ccp4bb] Finding Homologs with Specific Residues Conserved

[Keller, Jacob]

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 of thing to do, and might change results slightly a la 
psi-BLAST.

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.