I'm looking for the posible modeling script which could do:

i - multiple sequence alignment of several sequences agains target sequence (for which experimental structure is exist) to detect common functional-relevant motifs in each sequence of ensemble

ii- select the aligned sequence from the ensemble

iii- make a homology model for this structure based on the provided experimental (reference) structure including S-S bridges and ligand's coppied from the reference.

Please provide me with simolple python example of such fussion of sequence analysis and homology modeling,

Best,

James S.