How do I do protein structure homology-modelling similar to SWISS-MODEL without using a web api for computing and only use online databases for searching templates? I would like to use python (I heard salilab modeller can do this in some way) to integrate this into another additional script. It would be good to actually just search the templates using a web database and do the automodel on my computer. Is there any good way to do this role? Please suggest a similar way to do this if this has some difficulties. Thank you.
I've used ITASSER for this in the past. Its written in Perl and C, but there aren't that many inputs to it so you could write a python wrapper if you desperately wanted to.
If you register (free for academics), you can download and install the software locally https://zhanglab.ccmb.med.umich.edu/I-TASSER/