BuildModel

This is the workhorse of FoldX mutation engine. This command ensures that whenever you are mutating a protein you always move the same neighbours in the WT and in the mutant producing for each mutant PDB a corresponding PDB for its WT (each mutation will move different neighbours and therefore you need different WT references). Build model requires a mutant-file to run. The minimal configuration file for BuildModel:

command=BuildModel
pdb=BM.pdb
mutant-file=individual_list.txt

It can be run using the command line:

FoldX --command=BuildModel --pdb=BM.pdb --mutant-file=individual_list.txt

The parameter numberOfRuns tells the algorithm how many times it should do the specified mutations. Normally it should be set to 1. However, sometimes it can be set to higher numbers (typically 5) to see if the algorithm has achieved convergence, or in other words if the solution offered is the optimal or a trapped solution. The option out-pdb is setted to true by default and can be use with commands as Pssm or PssmStability.

FoldX uses output-file as a tag to label different outputs from different commands in batch runs. After running BuildModel you'll get three files to look at. Given pdb=PDB.pdb the output files are.

  • Average_PDB_BM.fxout -> average energy of the different runs
  • Dif_PDB_BM.fxout -> energy difference between reference WT and the corresponding mutant
  • Raw_PDB_BM.fxout -> full energy decomposition for the WT references and the mutants
  • PdbList_PDB_BM.fxout -> names of all the mutants and the corresponding WT references

Output files contains the Gibbs energy of protein folding decomposed into the different terms used by FOLDX. The files Dif_, Average_ and Raw_ have same headers with the energy terms decomposition in Kcal/mol, the colums are:

Energy terms

Title energy_description
Pdb Pdb file
Total Energy This is the predicted overall stability of your protein
Backbone Hbond This the contribution of backbone Hbonds
Sidechain Hbond This the contribution of sidechain-sidechain and sidechain-backbone Hbonds
Van der Waals Contribution of the VanderWaals
Electrostatics Electrostatic interactions
Solvation Polar Penalization for burying polar groups
Solvation Hydrophobic Contribution of hydrophobic groups
Van der Waals clashes Energy penalization due to VanderWaals’ clashes (interresidue)
Entropy Side Chain Entropy cost of fixing the side chain
Entropy Main Chain Entropy cost of fixing the main chain
Sloop Entropy ONLY FOR ADVANCED USERS
Mloop Entropy ONLY FOR ADVANCED USERS
Cis Bond Cost of having a cis peptide bond
Torsional Clash VanderWaals’ torsional clashes (intraresidue)
Backbone Clash Backbone-backbone VanderWaals. These are not considered in the total
Helix Dipole Electrostatic contribution of the helix dipole
Water Bridge Contribution of water bridges
Disulfide Contribution of disulfide bonds
Electrostatic Kon Electrostatic interaction between molecules in the precomplex
Partial Covalent Bonds Interactions with bound metals
Energy Ionisation Contribution of ionisation energy
Entropy Complex Entropy cost of forming a complex
Residue Number Number of residues

 

 

Parameter Description Default value
fix-residues-file is a text file where the residues we do not want to move should be detailed as in the individual_list format
moveNeighbours set to move neighbours when we mutate true
mutant-file File containing the desired mutations mutant_file.txt
numberOfRuns set the number of runs done in BuildModel or DNAScan 1
out-pdb set to output PDBs when doing mutations true
pdbDummys output the the dummy atoms we use (for N and C caps of helixes as well as the free orbitals) in the generated pdbs false
pdbHydrogens output the hydrogens we place in the generated pdbs false
pdbIsoforms output the isoforms of the His in the generated pdbs false
wildtype Wild type sequence for BuildModel