The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
Prediction of water and metal binding sites and their affinities by using the Fold-X force field
Open accessAbstract
The empirical force field Fold-X was developed previously to allow rapid free energy calculations in proteins. Here, we present an enhanced version of the force field allowing prediction of the position of structural water molecules and metal ions, together called single atom ligands. Fold-X picks up 76% of water molecules found to interact with two or more polar atoms of proteins in high-resolution crystal structures and predicts their position to within 0.8 Å on average. The prediction of metal ion-binding sites have success rates between 90% and 97% depending on the metal, with an overall standard deviation on the position of binding of 0.3-0.6 Å. The following metals were included in the force field: Mg 2+ , Ca 2+ , Zn 2+ , Mn 2+ , and Cu 2+ . As a result, the current version of Fold-X can accurately decorate a protein structure with biologically important ions and water molecules. Additionally, the free energy of binding of Ca 2+ and Zn 2+ (i.e., the natural logarithm of the dissociation constant) and its dependence on ionic strength correlate reasonably well with the experimental data available in the literature, allowing one to discriminate between high- and low-affinity binding sites. Importantly, the accuracy of the energy prediction presented here is sufficient to efficiently discriminate between Mg 2+ , Ca 2+ , and Zn 2+ binding.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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
Self-citationGuerois, R., Nielsen, J. E., & Serrano, L. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00442-4 · Cited by 1,728
Self-citationTransition Metal Speciation in the Cell: Insights from the Chemistry of Metal Ion Receptors
Finney, L. A., & O'Halloran, T. V. (2003) · Science · doi:10.1126/science.1085049 · Cited by 1,100
Calmodulin structure refined at 1.7 Å resolution
Chattopadhyaya, R., Meador, W. E., Means, A. R., & Quiocho, F. A. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90324-d · Cited by 729
Feig, M., & Brooks, C. L. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.03.009 · Cited by 566
Håkansson, K., Carlsson, M., Svensson, L. A., & Liljas, A. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90531-n · Cited by 511
Structural Aspects of Metal Liganding to Functional Groups in Proteins
Glusker, J. P. (1991) · Advances in Protein Chemistry · doi:10.1016/s0065-3233(08)60534-3 · Cited by 452
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 443
Protein-DNA interactions: a structural analysis
Jones, S., van Heyningen, P., Berman, H. M., & Thornton, J. M. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2659 · Cited by 424
Engineering Novel Metalloproteins: Design of Metal-Binding Sites into Native Protein Scaffolds
Lu, Y., Berry, S. M., & Pfister, T. D. (2001) · Chemical Reviews · doi:10.1021/cr0000574 · Cited by 375
Cited by
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases
Szczepek, M., Brondani, V., Büchel, J., Serrano, L., Segal, D. J., & Cathomen, T. (2007) · Nature Biotechnology · doi:10.1038/nbt1317 · Cited by 501
Self-citationDrosophila screen connects nuclear transport genes to DPR pathology in c9ALS/FTD
Boeynaems, S., Bogaert, E., Michiels, E., Gijselinck, I., Sieben, A., Jovičić, A., De Baets, G., Scheveneels, W., Steyaert, J., Cuijt, I., et al. (2016) · Scientific Reports · doi:10.1038/srep20877 · Cited by 262
Self-citationAnalysis of the human E2 ubiquitin conjugating enzyme protein interaction network
Markson, G., Kiel, C., Hyde, R., Brown, S., Charalabous, P., Bremm, A., Semple, J., Woodsmith, J., Duley, S., Salehi-Ashtiani, K., et al. (2009) · Genome Research · doi:10.1101/gr.093963.109 · Cited by 157
Self-citationBrender, J. R., & Zhang, Y. (2015) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004494 · Cited by 140
Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity
Li, M., Petukh, M., Alexov, E., & Panchenko, A. R. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct401022c · Cited by 111
Metadata
- Authors
- Schymkowitz, J. W. H., Rousseau, F., Martins, I. C., Ferkinghoff-Borg, J., Stricher, F., & Serrano, L.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2005-07-08
- Volume
- 102
- Issue
- 29
- Pages
- 10147-10152
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2098949725
- Cited by
- 339
- References
- 32
- FWCI
- 4.96
- Type
- journal article
- Language
- en
- Open access
- green
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Prediction of water and metal binding sites and their affinities by using the Fold-X force field. https://app.cochat.ai/papers/10.1073/pnas.0501980102
- The paper
- Schymkowitz, J. W. H., Rousseau, F., Martins, I. C., Ferkinghoff-Borg, J., Stricher, F., & Serrano, L. (2005). Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0501980102
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
