Examples

A force field for energy calculations and protein design

FoldX

Examples of FoldX calculations

Warning regarding energies:

The absolute energies are not precise
FoldX is accurate for relative energies
The total energy of a protein can be quite large for large proteins, as the total energy represents the energy of the total and not the energy of the composing domains (as experimental total energy)

Repair the PDB

Example: Repair of the pdb 1shg
PDB file: 1shg.pdb
list of PDB: list.txt
Runfile: run.txt
Result files:
- RepairPDB_1shg.pdb
- RepairPDB_1shg.fxout

Repair the PDB keeping one residue fixed

Example: Repair of the pdb 1shg keeping LYS39 fixed
PDB file: 1shg.pdb
list of PDB: list.txt
Runfile: run.txt
Result files:
- RepairPDB_1shg.pdb
- RepairPDB_1shg.fxout

Energy of the molecule

Example: Calculation of the energy of PDB 1shg
PDB file: RepairPDB_1shg.pdb
list of PDB: list.txt
Runfile: run.txt
Result files:
- Stability.txt

Interaction energy of two molecules

Mutation of selected position to groups of residues

Example: Position scan of PDB 1SHG
PDB file: 1shg.pdb
list of PDB: list.txt
Runfile: run.txt
Result files:

Multiple mutations using mutant file

Multiple mutations using indivudal list