Stability

Calculates the DG to fold the proteins from their unfolded state. The minimal configuration file for Stability is:

command=Stability
pdb=ST.pdb

It can be run from the command line:

FoldX --command=Stability --pdb=ST.pdb

FoldX uses output-file as a tag to label different outputs from different commands in batch runs. After running Stability you'll get one file to look at. Given output-file="TAG" the output file is:

TAG_ST.fxout -> calculates the different DG energy terms of folding the protein

If you don't set output-file, TAG will be the pdbId of the first pdb on the batch. Output file contains the Gibbs energy of protein folding decomposed into the different terms used by FOLD-X. This file will have different headers and then rows (one for each PDB run) with the energy decomposition in Kcal/mol, the different columns are described below in the table Energy Terms:

Energy terms

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

 

 

Parametersort descending Description Default value
complexWithRNA set it to true when you are working with RNA complexes false