FoldX

FoldX calculates protein folding energies and predicts the effects of point mutations on protein stability and on protein–ligand and protein–RNA interactions.

Key Features:

• Protein folding energy calculation: Computes folding energies from structural models for quantitative stability assessment.
• Mutation effect prediction: Predicts changes in protein stability caused by point mutations.
• RNA structure compatibility: Processes structures containing RNA molecules to enable analysis of RNA–protein complexes.
• Parametrization of ligands (ParamX): Includes the ParamX module to parametrise ligands and small molecules not previously recognised, enabling their inclusion in energy calculations.
• Custom molecule definitions (JSON): Accepts custom molecule parametrizations encoded in JSON for incorporation into analyses.

Scientific Applications:

• Protein Engineering: Predicts mutation effects on stability to guide design of proteins with altered properties.
• Drug Discovery: Enables modelling of protein–ligand interactions using parametrised ligands to support identification and optimisation of candidate compounds.
• RNA–Protein Interaction Studies: Supports analysis of stability and dynamics of RNA–protein complexes by processing RNA-containing structures.

Methodology:

Employs computational algorithms to simulate protein folding and to predict changes in stability due to point mutations or ligand binding.