Modeller mutate.py script
This modelling way uses the Modeller mutate.py script, available at Modeller's website. This script applies punctual replacements, has higher precision because doesn't change the protein conformation, but it is slower, since applies one mutation at a time.
Modeller standard fast model
Modeller's mutate.py doesn't apply deletions, then we generate a mutated sequence of the input complex, and E-Volve uses the Modeller standard fast model procedure to create a model of the mutated protein, using the mutated sequence and the input structure as a template.
The software search for possibles matches between contacts, after, refine and select the bests matches for this reason, the bigger the input file(in number of atoms), or the bigger the similarity between then more time is taken to find all possible contact and more time is taken for the refinment.
The loading page wait up to 30 minutes for the match completish, but some times the match process takes longer, so a "Time Out" alert is showed and the user recieves a link to try to access the alignment in future.