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

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1. Using RepairPDB to remove bad torsion angles and van der Waal’s clashes from the PDB file
2. Using BuildModel to compute the differences in protein stabilities between the template and the mutant

./foldx64Linux -runfile repairPDB.txt

./foldx64Linux -runfile foldx_run.txt

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