On 6/17/24 12:31 AM, Kyle- richard Dawson wrote: > Lastly, I would just like to know about how > modeller tackles the protein interface. Is it able to model the subunit > interactions if I only use duplicate chain templates? Since my protein > is a homodimer and the subunits are identical, I was hoping to use just > the best chain of each template but I worry that modeller might not be > able to discern the subunit interactions if I do so.
Short answer: no, not the way you're doing it. Modeller extracts distances from each template. If you only give it monomeric templates, it has no information about the interface between the two chains. You'll need to provide at least one template which spans the interface, or provide other distance restraints. See also https://salilab.org/modeller/10.4/manual/node29.html
Ben Webb, Modeller Caretaker