Hi Mijiddorj,
My target protein size is around 250 residues. It's pretty small and i
don't have issue with time. Can you please let me know the actual command
line for cluster analysis?
Regards!
On Thu, Dec 22, 2016 at 12:59 AM, Mijiddorj Batsaikhan <
b.mijidd...@gmail.com> wrote:
> Hi,
>
> Wha
Hi,
What is your target structure size? If you want to perform explicit solvent
simulation for bigger protein, it may be time-consuming simulation.
My suggestion is that you can run simulation implicitly, it helps you
remove some bad contacts. Then, you can make cluster analysis and find
dominatin
Hi Mark,
Thanks for your response. I did for simulation for both the systems 1. only
protein 2. protein with co-factor. By the way, I'm not pretty sure, but I'm
relying on rmsd of C-alpha to evaluate the structure's stability. In both
the cases, the rmsd range was highly wide ~3-6 nm. Then i super
Hi,
On Thu, Dec 22, 2016 at 5:19 PM Amir Zeb wrote:
> Hi Mark,
>
> I want to refine the model for any bad contact if the structure has.
So, do you expect the structure to be stable in the absence of the other
things? That tells you whether you need to attempt refinement with the
other things,
Hi Mark,
I want to refine the model for any bad contact if the structure has. This
article support the simulation of any homology model after its creation by
homology modeling approach "
https://www.ncbi.nlm.nih.gov/pubmed/22513870?dopt=Abstract";. Do you please
think that there is no need to refi
Hi,
What us the purpose in doing MD on the homology model? That'll tell you
whether you need a model with the other parts.
Mark
On Thu, 22 Dec 2016 16:51 Amir Zeb wrote:
> Hello,
>
> I have created a homology model for a protein, where the seq. identity
> between the template and target is 40%
Hello,
I have created a homology model for a protein, where the seq. identity
between the template and target is 40%. The template structure also
contains co-factor and an inhibitor in bound form means it is a complex.
I'll have to define the ligand binding site in target (homology model)
based on
