Dear Ben,

Thank you very much for your email.

We are modelling 80 isoforms of an enzyme superfamily. In the 1st step we generated the models based on the templates that have higher sequence identity. Now, we are trying to place a loop in a specific conformation. This loop is very important for the enzyme catalysis.  The catalytic site is build up by a Calcium center coordinated with 6 residues. 4 of those are located in the loop that does not have the desired conformation. Our problem is due to the fact that the most of the templates (selected based on their higher identity to the target) did not have calcium in the X-ray structure which displaces the loop. What we are trying now is to refine this problemic region in order to match the only X-ray structure that was solved in presence of Calcium and obtain the ideal conformation for the active enzyme. Do you have any suggestions on how we could achieve this using modeller?

Best,

Miguel   

Enviado do Correio para Windows 10

De: Modeller Caretaker
Enviado: 22 de abril de 2021 18:21
Para: Miguel Lacerda; modeller_usage@salilab.org
Assunto: Re: [modeller_usage] Do a loop refinment in order to mimic loop in a template

On 4/22/21 7:24 AM, Miguel Lacerda wrote:
> Is it possible to do a loop refinment of a model by giving the residue
> range plus the template (which will hold the desired spatial location)?

If you already know the "desired spatial location" then what are you
trying to refine?

> The orientation of the loop in my model its different to  my template’s.

Modeller does not use the template orientation for loops (many loops
correspond to insertions anyway). The starting conformation for a loop
is random and is influenced only by the termini positions. See the loop
modeling paper or https://salilab.org/modeller/10.1/manual/node499.html

If you want to manually set the starting conformation for the loop,
override the build_ini_loop() method:
https://salilab.org/modeller/10.1/manual/node96.html

        Ben Webb, Modeller Caretaker
--
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