foldx.assembly: Compute Assembly Free Energy

In ptm: Analyses of Protein Post-Translational Modifications

Compute Assembly Free Energy

Description

Computes changes in the Gibbs free energy of the assembly process of a protein.

Usage

foldx.assembly(pdb, mol1, mol2, pH = 7, I = 0.05)

Arguments

pdb	the 4-letter identifier of a PDB structure or the path to a PDB file.
mol1	molecule or group of molecules interacting with mol2 (see details)
mol2	molecule or group of molecules interacting with mol1 (see details)
pH	a numeric value between 0 and 14.
I	a value indicating the molar ionic strength.

Details

This function implements the FoldX's command 'AnalyseComplex', which allows to determine the interaction energy between two molecules or two groups of molecules. For instance, if in a dimeric protein, formed by chain A and B, we may set: mol1 = 'A', mol2 = 'B'. If we are dealing with a trimer, we may set: mol1 = 'A', mol2: 'AB'.

Value

The function returns a dataframe with the residues that make up the interface between mol1 and mol2, as well as the change in Gibbs free energy, DG, of the assembly process for the requested subunits.

Author(s)

Juan Carlos Aledo

References

Schymkowitz et al (2005) Nucl. Ac. Res. 33:W382-W388.

See Also

foldx.stab()

Examples

## Not run: foldx.assembly(pdb = '1sev', mol1 = 'A', mol2 = 'B')

ptm documentation built on Aug. 7, 2022, 5:05 p.m.