Hello,

I just want to point out that, especially as the missing loop is close
to the active site and can reach it directly, presumably it could play a
significant role in gatekeeping, activation, stabilization of the bound
state, etc. Thus, one probably has to take care in interpreting the
resulting model because any specific conformation of the loop will be
more or less random and not necessarily relevant to a particular state
of a protein. Perhaps the dynamics of the loop (with and without bound
ligands) should be further analyzed.

Best regards
Eugene

On 15.12.2021 05:06, Modeller Caretaker wrote:
> On 12/14/21 6:22 AM, Karki, Sudeep wrote:
>> I have a structure with a small molecule bound in the active site.
>> There are missing residues in the structure, how can I model it? I
>> tried without the small molecule but it forces the neighbor loop to
>> go in the active site and definitely I don´t want that.
>
> Just add the residues that are missing in your template structure to
> the target sequence, aligned with gaps in the template. One example is at
> https://salilab.org/modeller/wiki/Missing%20residues
>
>     Ben Webb, Modeller Caretaker
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