1. Structure-based sequence alignment
2. Building a homology model based on aligned sequences
Template sequence — 1LAF.ali Template PDB structure — 1LAF.pdb Mutant sequence — 1LAF_mutant.ali
modeller9.11/bin/modpy.sh python align.py -t 1LAF -m 1LAF_mutant
modeller9.11/bin/modpy.sh python md-model-build-dope.py -t 1LAF -m 1LAF_mutant
#####################################################################################
- Using RepairPDB to remove bad torsion angles and van der Waal’s clashes from the PDB file
- Using BuildModel to compute the differences in protein stabilities between the template and the mutant
./foldx64Linux -runfile repairPDB.txt
./foldx64Linux -runfile foldx_run.txt
#####################################################################################