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The FoldX web server: an online force field
Open accessAbstract
FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at http://foldx.embl.de/. The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed.
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“The empirical energy-based methods, exemplified by STATIUM [12], FoldX [8] and Discovery Studio [13], have accelerated the prediction but suffered from insufficient conformational sampling, especially for mutations in flexible regions.”
From Deep geometric representations for modeling effects of mutations on protein-protein binding affinity (2021) · cites this paper as [8]
In the citing paper
“We observed FoldX [8] and BeAtMuSic [38] yield the lowest correlations and the highest root-mean-square error (RMSE) on these datasets, indicating the difficulty of gauging the impacts of mutations via empirical energy-based methods.”
From Deep geometric representations for modeling effects of mutations on protein-protein binding affinity (2021) · cites this paper as [8]
In the citing paper
“Previous methods were limited either in terms of their throughput (21,22) or in terms of their performance (23).”
From mCSM-PPI2: predicting the effects of mutations on protein–protein interactions (2019) · cites this paper as [22]
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“Although the pdb-reader in FoldX is continually extended to handle more exceptions, standardizing the format of anomalous files most often solves the problem—this can easily be achieved by opening and saving the file using Swiss PDB viewer (14) or WHATIF (15).”
MethodThe interpretation of protein structures: Estimation of static accessibility
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“The occupancy of an atom i, Occ(i), is calculated using an envelope function (21) with a distance cut-off of 6 s (9).”
MethodWHAT IF: A molecular modeling and drug design program
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“Although the pdb-reader in FoldX is continually extended to handle more exceptions, standardizing the format of anomalous files most often solves the problem—this can easily be achieved by opening and saving the file using Swiss PDB viewer (14) or WHATIF (15).”
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BackgroundMethodInfluentialSelf-citationPrediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
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“In this fashion, TANGO predicts correctly both the disease causing and protective mutations in a wide range of proteins including Alzheimers’ A b peptide, lysozyme and transthyretin (12).”
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“The statistical mechanics algorithm TANGO, publicly available at http:// TANGO.embl.de/, provides such a predictive model.”
MethodInfluentialMolecular basis for amyloid fibril formation and stability
Makin, O. S., Atkins, E. D. T., Sikorski, P., Johansson, J., & Serpell, L. C. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406847102 · Cited by 649 · cited 1×
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BackgroundEffective energy functions for protein structure prediction
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“Sci. 2016, 17, 547 3 of 11 the performance of existing solutions, including BeAtMuSiC [30] and FoldX [31].”
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Metadata
- Authors
- Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L.
- Affiliations
- Vrije Universiteit Brussel (BE)
- University of Copenhagen (DK)
- European Molecular Biology Laboratory (DE)
- Corresponding author
- Schymkowitz, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-07-01
- Volume
- 33
- Issue
- Web Server
- Pages
- W382-W388
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1160148
- OpenAlex
- W2023490488
- Semantic Scholar
- 18ceb01ed1614dfc42404e0e2d838443cc0a4731
- Cited by
- 2,759
- References
- 23
- Citations by year
- 2026: 222 · 2025: 298 · 2024: 254 · 2023: 264 · 2022: 215 · 2021: 227 · 2020: 223 · 2019: 181 · 2018: 150 · 2017: 113 · 2016: 99 · 2015: 96 · 2014: 90 · 2013: 65 · 2012: 65
- FWCI
- 9.29
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Funders
- European Commission
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- FoldX, empirical force fields, protein stability, free energy calculation, protein folding, protein dynamics, nucleic acids, mutation effects, proton positions, water bridges, metal binding sites, complex formation, alanine scanning
- MeSH terms
- Mutation, Nucleic Acid Conformation, Protein Conformation, Proteins, Software, Molecular Structure, Protein Folding, Internet, Polymorphism, Single Nucleotide, Databases, Protein
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