Re: [modeller_usage] Modelling missing residues

To: Eugene Radchenko <>, "" <>

Subject: Re: [modeller_usage] Modelling missing residues

From: "Karki, Sudeep" <>

Date: Wed, 15 Dec 2021 12:36:27 +0000

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Thank you all for the suggestions.The missing residues are near the active site. These missing residues are supposed to be unstructured and in the cryo-EM map I cannot see the density - basically can’t model this region. Of course, the structure we have is with the small molecule bound and for MD work I would like to get the complete structure. Is there any way the modeler can read “HEATOM” - so that I could model the missing residues using the small molecule bound structure as input in modeler. Earlier,I removed the small molecule and tried to build the complete model in Modeller - in this case, the missing residue formed a loop and was placed in the small molecule binding region that is wrongly placed . I agree that the dynamics of the loop with and without bound ligands need to be further analyzed.

Sudeep

From: modeller_usage <> on behalf of Eugene Radchenko <>
Sent: Wednesday, December 15, 2021 12:46 PM
To: <>
Subject: Re: [modeller_usage] Modelling missing residues

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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