The DOI matches its Crossref record; 76 of the 76 references it cites were found in a registry or an index.
Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
Open accessAbstract
Recent advances in high-throughput experimental methods for the identification of protein interactions have resulted in a large amount of diverse data that are somewhat incomplete and contradictory. As valuable as they are, such experimental approaches studying protein interactomes have certain limitations that can be complemented by the computational methods for predicting protein interactions. In this review we describe different approaches to predict protein interaction partners as well as highlight recent achievements in the prediction of specific domains mediating protein-protein interactions. We discuss the applicability of computational methods to different types of prediction problems and point out limitations common to all of them.
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
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
The comparative method in evolutionary biology
(1992) · Choice Reviews Online · doi:10.5860/choice.29-5104 · Cited by 4,931
The Comparative Method in Evolutionary Biology
Harvey, P. H., & Pagel, M. D. (1991) · doi:10.1093/oso/9780198546412.001.0001 · Cited by 4,337
Pfam: clans, web tools and services
Finn, R. D. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj149 · Cited by 2,302
Detecting Protein Function and Protein-Protein Interactions from Genome Sequences
Marcotte, E. M., Pellegrini, M., Ng, H.-L., Rice, D. W., Yeates, T. O., & Eisenberg, D. (1999) · Science · doi:10.1126/science.285.5428.751 · Cited by 1,670
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., & Yeates, T. O. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.8.4285 · Cited by 1,585
A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data
Jansen, R., Yu, H., Greenbaum, D., Kluger, Y., Krogan, N. J., Chung, S., Emili, A., Snyder, M., Greenblatt, J. F., & Gerstein, M. (2003) · Science · doi:10.1126/science.1087361 · Cited by 1,254
The use of gene clusters to infer functional coupling
Overbeek, R., Fonstein, M., D’Souza, M., Pusch, G. D., & Maltsev, N. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.6.2896 · Cited by 1,241
Conservation of gene order: a fingerprint of proteins that physically interact
Dandekar, T. (1998) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(98)01274-2 · Cited by 1,041
Kernel Methods in Computational Biology
(2004) · The MIT Press eBooks · doi:10.7551/mitpress/4057.001.0001 · Cited by 1,032
Cited by
Structure-based prediction of protein–protein interactions on a genome-wide scale
Zhang, Q. C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C. A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., et al. (2012) · Nature · doi:10.1038/nature11503 · Cited by 723
Ovchinnikov, S., Kamisetty, H., & Baker, D. (2014) · eLife · doi:10.7554/elife.02030 · Cited by 629
Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases
Shoemaker, B. A., & Panchenko, A. R. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030042 · Cited by 398
Self-citationGlobal Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
Hu, P., Janga, S. C., Babu, M., Díaz-Mejía, J. J., Butland, G., Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000096 · Cited by 387
Computational prediction of protein–protein binding affinities
Siebenmorgen, T., & Zacharias, M. (2020) · WIREs Computational Molecular Science · doi:10.1002/wcms.1448 · Cited by 184
“5,6 Within different protein families, these domains can differ in sequence resulting in different binding specificities and in different combinations of possible interactions.”
Background
Metadata
- Authors
- Shoemaker, B. A., & Panchenko, A. R.
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2007-04-27
- Volume
- 3
- Issue
- 4
- Pages
- e43
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W2029574260
- Cited by
- 332
- References
- 76
- FWCI
- 11.02
- Type
- journal article
- Language
- en
- Open access
- gold
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: Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners. https://app.cochat.ai/papers/10.1371/journal.pcbi.0030043
- The paper
- Shoemaker, B. A., & Panchenko, A. R. (2007). Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.0030043
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.
