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Abstract
Motivation
The 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.
Results
These 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/.
Academic Publication FoldX force field revisited, an improved version
Research Abstract & Technology Focus
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FoldX force field revisited, an improved version
Abstract Motivation The FoldX force field was originally validated with a database of 1000 mutants at a time when there were few high-resolution ...
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Frequently Asked Questions (FAQ)
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What is the core focus of the research titled 'FoldX force field revisited, an improved version'?
This literature focuses on: Abstract Motivation The 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 datab...
Are there open-source GitHub repositories related to FoldX force field revisited, an improved version?
Yes, open-source projects like afar1/fieldtheory-cli (Sync and locally store all of your X/Twitter bookmarks. Free and open source CLI for Mac.) are actively building upon these concepts.
Which startups are commercializing the technology behind FoldX force field revisited, an improved version?
Products like Katalyst are bringing this to market. Their focus is: The AI agent that works your Salesforce Pipeline.
What other academic literature is closely related to 'FoldX force field revisited, an improved version'?
Yes, highly correlated activity was mapped. An entry titled 'FoldX force field revisited, an improved version' discusses this: Abstract Motivation The FoldX force field was originally validated with a database of 1000 muta...
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GitHubafar1/fieldtheory-cli
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GitHubGammaLabTechnologies/harmonist
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