Hello. I have an original pdb file of each of some enzyme proteins. I also have pdb files that I have built using homology modelling after making some mutations with the fasta sequrnces. I would like to check if the mutated enzymes still do their functions on their active sites using a computer program. Programs like TM-Score and etc show very similar scores even if there are a substancial amount of mutations. How should I do this efficiently and with a mininum amount of error? This is only for prediction before actually doing wet lab, but it should be efficient enough.
Thank you very much in advance.
Thank you for the recommendation. Is it possible to automate the process using for example python subprocess module with vina?
I don't see why not. I have never done it myself so can't give you specifics, but I believe it has a commandline interface. You need not even necessarily appeal to Python to do it. Some simple shell scripting should allow you to launch several docking jobs at once if that is all you want to do.
Alternatively, UCSF Chimera is written mostly in python, and has a Docking module you could make use of. Their documentation is extensive, so I won't even attempt to delve in to detail here.