I am totally new to this in silico! We have protein (with known X-ray structure) consisting of 2 domains (A and B) loosely held by a few helices+sheet (may be considered as a small 3rd 'C' domain). I run pmut_scan_parallel. Runs through all residues finding the mutations. We are especially interested on the interface between A-B and B-C . Sort the result by free energy change (average_ddG). Some the suggested mutants are very specific interactions that seems to be important - and seem to stablize the interactions. Has any such work done before on such a *multidomain* protein?
We are wondering if this can be used as a superior alternative to alanine scanning. Any suggestions gratefully accepted.
pmut_scan_parallel.static.linuxgccrelease -database \
-s alldomains.pdb -DDG_cutoff 1000000000000 \
-ex1 -ex2 -ex3 -extrachi_cutoff 1 -use_input_sc -ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -mute basic core | tee scan_for_all.log