The DOI matches its Crossref record; 94 of the 95 references it cites were found in a registry or an index.
Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations
Abstract
We have developed a computer algorithm, FOLDEF (for FOLD-X energy function), to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. The predictive power of FOLDEF was tested on a very large set of point mutants (1088 mutants) spanning most of the structural environments found in proteins. FOLDEF uses a full atomic description of the structure of the proteins. The different energy terms taken into account in FOLDEF have been weighted using empirical data obtained from protein engineering experiments. First, we considered a training database of 339 mutants in nine different proteins and optimised the set of parameters and weighting factors that best accounted for the changes in stability of the mutants. The predictive power of the method was then tested using a blind test mutant database of 667 mutants, as well as a database of 82 protein-protein complex mutants. The global correlation obtained for 95 % of the entire mutant database (1030 mutants) is 0.83 with a standard deviation of 0.81 kcal mol(-1) and a slope of 0.76. The present energy function uses a minimum of computational resources and can therefore easily be used in protein design algorithms, and in the field of protein structure and folding pathways prediction where one requires a fast and accurate energy function. FOLDEF is available via a web-interface at http://fold-x.embl-heidelberg.de
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“They usually take a form of linear functions, often with only energy‐based terms, and fail to exploit evolution information, which can limit their ability to capture mutation effects on binding affinity.”
From iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations (2019) · cites this paper as [6]
Citations
Cites
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
Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., et al. (2000) · Accounts of Chemical Research · doi:10.1021/ar000033j · Cited by 4,978
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
Proteins: Structures and Molecular Properties
Creighton, T. E. (1986) · Medical Entomology and Zoology · Cited by 2,645
Why are ?natively unfolded? proteins unstructured under physiologic conditions?
Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20001115)41:3 · Cited by 2,097
The Solubility of Amino Acids and Two Glycine Peptides in Aqueous Ethanol and Dioxane Solutions
Nozaki, Y., & Tanford, C. (1971) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)77210-x · Cited by 1,430
Proteins. Structures and molecular properties
(1984) · Analytical Biochemistry · doi:10.1016/0003-2697(84)90583-9 · Cited by 1,308
A simplified representation of protein conformations for rapid simulation of protein folding
Levitt, M. (1976) · Journal of Molecular Biology · doi:10.1016/0022-2836(76)90004-8 · Cited by 1,123
Abagyan, R. A., & Totrov, M. M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1052 · Cited by 982
Itzhaki, L. S., Otzen, D. E., & Fersht, A. R. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0616 · Cited by 750
Cited by
Sorted by citations
The FoldX web server: an online force field
Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki387 · Cited by 2,759
“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-citationI-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
Capriotti, E., Fariselli, P., & Casadio, R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki375 · Cited by 2,079
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
Self-citationHarnessing protein folding neural networks for peptide–protein docking
Tsaban, T., Varga, J. K., Avraham, O., Ben-Aharon, Z., Khramushin, A., & Schueler-Furman, O. (2022) · Nature Communications · doi:10.1038/s41467-021-27838-9 · Cited by 1,205
Prediction of protein stability changes for single‐site mutations using support vector machines
Cheng, J., Randall, A. Z., & Baldi, P. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20810 · Cited by 1,170
Metadata
- Authors
- Guerois, R., Nielsen, J. E., & Serrano, L.
- Affiliations
- Howard Hughes Medical Institute (US)
- European Molecular Biology Laboratory (DE)
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2002-07
- Volume
- 320
- Issue
- 2
- Pages
- 369-387
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2092387745
- Cited by
- 1,728
- References
- 95
- Citations by year
- 2026: 68 · 2025: 85 · 2024: 61 · 2023: 78 · 2022: 74 · 2021: 90 · 2020: 98 · 2019: 82 · 2018: 90 · 2017: 84 · 2016: 94 · 2015: 93 · 2014: 90 · 2013: 102 · 2012: 87
- FWCI
- 12.09
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- protein stability prediction, point mutations, protein-protein complex, parameter optimization, protein design, protein folding pathways
- MeSH terms
- Algorithms, Hydrogen Bonding, Models, Genetic, Mutation, Protein Conformation, Proteins, Software, Thermodynamics, Water, Models, Statistical, Point Mutation, Protein Structure, Secondary, Protein Folding, Databases as Topic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
