Re: [modeller_usage] Modelling missing residues

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