ArticleBioinformatics (Oxford, England)2025
FoldX force field revisited, an improved version.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
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- AGGRESCAN and its evolution: A two-decade perspective on protein aggregation prediction.Biophysical reviews · 2026Review
- iDLDDG: predicting protein stability changes from missense mutations in DNA-binding proteins using integrated deep learning features.Briefings in bioinformatics · 2026Article
- FireProtDB 2.0: large-scale manually curated database of the protein stability data.Nucleic acids research · 2026Article
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8 authors.
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Abstract
motivationThe FoldX force field was originally validated with a database of 1000 mutants at a time when there were few high-resolution structures. Here, we have manually curated a database of 5556 mutants affecting protein stability, resulting in 2484 highly confident mutations denominated FoldX stability dataset (FSD), represented in non-redundant X-ray structures with <2.5 Å resolution, not involving duplicates, metals, or prosthetic groups. Using this database, we have created a new version of the FoldX force field by introducing pi stacking, pH dependency for all charged residues, improving aromatic-aromatic interactions, modifying the Ncap contribution and α-helix dipole, recalibrating the side-chain entropy of methionine, adjusting the H-bond parameters, and modifying the solvation contribution of tryptophan and others.
resultsThese changes have led to significant improvements for the prediction of specific mutants involving the above residues/interactions and a statistically significant increase of FoldX predictions, as well as for the majority of the 20 aa. Removing all training sets data from FSD [Validation FoldX Stability Dataset (VFSD) dataset] resulted in improved predictions from R = 0.693 (RMSE = 1.277 kcal/mol) to R = 0.706 (RMSE = 1.252 kcal/mol) when compared with the previously released version. FoldX achieves 95% accuracy considering an error of ±0.85 kcal/mol in prediction and an area under the curve = 0.78 for the VFSD, predicting the sign of the energy change upon mutation. AVAILABILITY AND IMPLEMENTATION: FoldX versions 4.1 and 5.1 are freely available for academics at https://foldxsuite.crg.eu/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.