What is FoldX?
FoldX is a protein modeling / design tool (originally developed at the Centre for Genomic Regulation (CRG) / VIB / SWITCH lab, led by Luis Serrano and collaborators) that uses an empirical force field to evaluate stability, interactions, and effects of mutations in proteins, protein–protein complexes, and protein-DNA complexes.
Key Features
FoldX is relatively fast, using a full‐atom structural description plus empirical energy terms, making it suitable for scanning many potential mutations or variants.
- Quantitative estimation of how mutations affect protein stability (folding free energy changes).
- Analysis of protein-protein and protein-DNA interaction energies.
- Alanine‐scanning (in silico) — mutating interface residues to alanine to estimate their contribution to binding or stability.
- Parametrization of small molecules or custom ligands (in more recent versions), supporting more complex designs and interactions.
How FoldX Works?
FoldX uses a force field combining multiple energy terms designed from empirical data plus some theoretical approximations. Some of its main components:
| Component |
What It Models |
Why It Matters |
| Van der Waals interactions |
How atoms pack & repel/attract each other in the folded state |
Ensure good packing, avoids clashes; contributes to stability |
| Solvation energies (hydrophobic / hydrophilic) |
Effect of water, exposure vs burial of residues |
Hydrophobic collapse, polar interactions; key for folding & binding |
| Hydrogen bonds |
Stabilizing polar interactions (backbone or side‐chain) |
Critical for geometry, fold integrity |
| Electrostatics |
Charge-charge and charge-polar interactions, salt bridges |
Affect both stability and binding specificity |
| Entropic cost of side-chains / backbone |
Penalize fixing parts of the protein / ordering them |
Real proteins lose entropy upon folding or binding; balance with favorable interactions |
| Interaction free energies (for complexes) |
Difference between bound vs unbound states |
Predict affinity & binding strength |
FoldX uses a rotamer library to sample side‐chain conformations, and can optimize side chains around mutations. It also has tools for repairing structures (e.g. Fixing side-chain conformations), calculating residue-level contributions, scanning mutations, analyzing complexes, etc.
Pharmaceutical & Biotech Applications of FoldX
FoldX has many applications in pharma and related industries, particularly where understanding or optimizing protein stability, interactions, mutations, or binding is essential. Some examples:
| Application |
Use Case / Benefit |
| Mutational Effect Prediction |
Predict how single‐point mutations (e.g. SNPs, disease variants) change folding stability or binding, helping to prioritize which ones are likely deleterious; useful in understanding genetic diseases or engineering safer/more stable therapeutics. |
| Protein Engineering / Stability Optimization |
Improve the thermal stability, shelf-life, resistance to degradation, expression yield etc., of therapeutic proteins (e.g. enzymes, monoclonals) by scanning candidate mutations in silico with FoldX to pick promising ones. |
| Affinity & Specificity Modulation |
Modifying interface residues (via alanine scanning or more directed mutation) to alter how strongly two proteins or a protein and ligand interact; used for designing better binders, inhibitors, or to reduce off-target binding. |
| Protein–DNA Interface Engineering |
Designing DNA‐binding proteins or transcription factor modifications; FoldX has been used in modeling zinc finger nucleases binding specific DNA sequences by correlating binding energy predictions to functional outcomes. |
| Small Molecule / Ligand Parametrization |
FoldX 5.0 has the ability to work with custom ligands or RNA, allowing modeling of small molecule binding, ligand design or assessing binding of non‐protein partners. |
| Rapid Screening of Variants |
In drug development pipelines where many mutant or variant proteins need to be tested (for example, evolving resistance or screening many antibody variants), FoldX gives fast approximate energy predictions to focus experimental effort. |
| Quality Control / Structural Assessment |
Checking whether proposed mutations or engineering efforts introduce structural instability or unfavorable interactions; assessing if models (e.g. experimental or predicted) have unrealistic interactions, clashes, etc. |
Strengths
- Fast and many‐mutation capable.
- Detailed residue‐level breakdowns of energetic contributions.
- Good for known proteins / complexes where you have a good high‐resolution structure.
- Useful for early-stage design to narrow down candidates.
Limitations
- Accuracy depends heavily on the input structure quality; bad structure or missing loops can degrade predictions.
- Empirical force field: some physics approximations, may not capture all entropic, conformational flexibility, or long‐range dynamics.
- Not as good for large conformational changes, large induced fit, or highly flexible regions.
- Predictions are approximations; need experimental validation.
Related Services
Structure Modeling Service
Antibody-Antigen Interaction Modeling Service
Reverse Docking Service
Rigid Docking Service
Peptide Folding Simulation Service
* For Research Use Only.
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