poli.objective_repository.foldx_stability_and_sasa.register

Registers the stability and SASA FoldX black box and objective factory.

FoldX [1] is a simulator that allows for computing the difference in free energy between a wildtype protein and a mutated protein. We pair this with biopython [2] to compute the SASA of the mutated protein.

[1] Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F.,

& Serrano, L. (2005). The FoldX web server: an online force field. Nucleic acids research, 33(suppl_2), W382-W388.

[2] Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I,

Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423

Classes

FoldXStabilityAndSASABlackBox(wildtype_pdb_path)	A black box implementation for computing the solvent accessible surface area (SASA) score using FoldX.
FoldXStabilityAndSASAProblemFactory()	Factory class for creating FoldX SASA (Solvent Accessible Surface Area) problems.