Cited by 2,759Protein Structure and DynamicsEnzyme Structure and FunctionRNA and protein synthesis mechanisms

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The FoldX web server: an online force field

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Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., Serrano, L.·2005·Nucleic Acids Research

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Abstract

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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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 11,297 · 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).”
Method
The 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).”
Method
WHAT 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).”
Method
Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations
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“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-citation
Prediction 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-citation
Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins
Abagyan, 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.”
MethodInfluential
Molecular 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).”
Background
Effective 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.”
Background
Protein-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.”
Background
Rational 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

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Self-citation

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.
ORCID: Schymkowitz, J.
Stricher, F.
Nys, R.
Rousseau, F.
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
DOI: 10.1093/nar/gki387
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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