This command is used to predict the binding energy of different metals to proteins and DNA. It is used with together with the option metal and metal_element. The minimal configuration file for MetalBinding is:
command=MetalBinding pdb=MB.pdb
It can be run from the command line:
FoldX --command=MetalBinding --pdb=MB.pdb
Depending on the chosen option in the “metal” parameter, this command can be used to either determine the interaction energy of crystal metals (CRYSTAL), optimize the crystal metals and then predict the binding energy (OPTIMIZE), or de novo predict binding sites and interaction energies of the selected ion (PREDICT).
PREDICT
This option will produce an output if a high affinity metal binding site is predicted. Output file: This option will produce an output if a high affinity metal binding site is predicted. The file will contain lines with the pdb name and the identity of the metal. In case that the predicted metal is close to an existing crystal one it will also print the coordinates of the crystal metal, the sum of the interactions with the protein, the coordinates of the predicted metal and the sum of its interactions with the protein and the decomposed binding energy of the predicted metal; “predict_output.txt” This file will contain lines with the pdb name, the identity of the metal and the binding energy.
OPTIMIZE
Output file: The file will contain lines with the pdb name, the identity of the metal, the coordinates of the crystal metal, the sum of the interactions with the protein, the coordinates of the optimized metal and the sum of its interactions with the protein and the decomposed binding energy of the optimized metal;
CRYSTAL
Output file: The file will contain lines with the pdb name, the identity of the metal and the decomposed metal binding energy in kcal/mol (positive numbers means high affinity) for the metals found in the crystal structure.
