The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
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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Citations
Cites
SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling
Guex, N., & Peitsch, M. C. (1997) · Electrophoresis · doi:10.1002/elps.1150181505 · Cited by 11,312 · cited 1×
“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
Lee, B., & Richards, F. M. (1971) · Journal of Molecular Biology · doi:10.1016/0022-2836(71)90324-x · Cited by 5,884 · cited 1×
“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
Vriend, G. (1990) · Journal of Molecular Graphics · doi:10.1016/0263-7855(90)80070-v · Cited by 3,476 · cited 1×
“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).”
MethodGuerois, R., Nielsen, J. E., & Serrano, L. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00442-4 · Cited by 1,728 · cited 3×
“In addition, those water molecules that have a persistent interaction with groups of the protein, i.e. make more than two hydrogen bonds with the protein, are calculated explicitly in the D G wb term (8,9).”
BackgroundMethodInfluentialSelf-citationPrediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
Fernández‐Escamilla, A. M., Rousseau, F., Schymkowitz, J. W. H., & Serrano, L. G. (2004) · Nature Biotechnology · doi:10.1038/nbt1012 · Cited by 1,667 · cited 1×
“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).”
BackgroundSelf-citationAbagyan, R. A., & Totrov, M. M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1052 · Cited by 982 · cited 8×
“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×
“For protein aggregation no such detail is available, although recently the first ever crystal structure of an amyloid fibre was released (23).”
BackgroundEffective energy functions for protein structure prediction
Lazaridis, T. (2000) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00063-4 · Cited by 445 · cited 1×
“These are designated by Lazaridis and Karplus (1) as statistical (SEEF) and physical (PEEF) effective energy functions, respectively.”
BackgroundProtein-misfolding diseases: Getting out of shape
Dobson, C. M. (2002) · Nature · doi:10.1038/418729a · Cited by 341 · cited 1×
“The crystal structure confirms the widespread observation in the field that protein aggregates are generally rich in cross-beta structure (24), which allows a low-resolution structural approach to predict protein aggregation.”
BackgroundRational design of faster associating and tighter binding protein complexes.
Schreiber, G., Selzer, T., & Albeck, S. (2000) · Nature Structural Biology · doi:10.1038/76744 · Cited by 299 · cited 1×
“(10), which was shown to give a good estimation of the association rate ( k on ) of complex formation.”
Background
Cited by
Sorted by citations
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Knijnenburg, T., Wang, L., Zimmermann, M. T., Chambwe, N., Gao, G. F., Cherniack, A. D., Fan, H., Shen, H., Way, G. P., Greene, C. S., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.076 · Cited by 1,145
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability
Rodrigues, C. H., Pires, D. E., & Ascher, D. B. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky300 · Cited by 1,086
Pi-Pi contacts are an overlooked protein feature relevant to phase separation
Vernon, R. M., Chong, P. A., Tsang, B., Kim, T. H., Bah, A., Farber, P. J., Lin, H., & Forman-Kay, J. D. (2018) · eLife · doi:10.7554/elife.31486 · Cited by 904
“F), Analysis of the relationship between the energetic effects of point mutations (DDG) and pi-contacts for experimental DDGs (blue bars) and DDGs predicted by simulation against the FOLDX force field (Schymkowitz et al., 2005) (C,E) and Rosetta (D,F).”
BackgroundMethodInfluentialExploring the sequence determinants of amyloid structure using position-specific scoring matrices
Maurer‐Stroh, S., Debulpaep, M., Kuemmerer, N., de la Paz, M. L., Martins, I. C., Reumers, J., Morris, K. L., Copland, A., Serpell, L. C., Serrano, L. G., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1432 · Cited by 700
“Therefore, we modeled a set of hexapeptides from amyloid-related disease proteins into available parallel and antiparallel fibril structures and evaluated their energy using Fold”
MethodSelf-citationWidespread macromolecular interaction perturbations in human genetic disorders
Sahni, N., Yi, S., Taipale, M., Fuxman Bass, J. I., Coulombe-Huntington, J., Yang, F., Peng, J., Weile, J., Karras, G. I., Wang, Y., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.013 · Cited by 594
“In addition, computational predictions by the FoldX program (Schymkowitz et al., 2005) suggest that mutant proteins with increased binding to QCFs are likely to be significantly less stable than their WT counterpart (Figure 3D and Table S2B).”
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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