Detecting Protein Function and Protein-Protein Interactions from Genome Sequences
Abstract
A computational method is proposed for inferring protein interactions from genome sequences on the basis of the observation that some pairs of interacting proteins have homologs in another organism fused into a single protein chain. Searching sequences from many genomes revealed 6809 such putative protein-protein interactions in Escherichia coli and 45,502 in yeast. Many members of these pairs were confirmed as functionally related; computational filtering further enriches for interactions. Some proteins have links to several other proteins; these coupled links appear to represent functional interactions such as complexes or pathways. Experimentally confirmed interacting pairs are documented in a Database of Interacting Proteins.
Integrity signals
Registry
Cites
Statistics
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?
Many proteins that form complexes in prokaryotes are fused into long, single-chain, multidomain proteins in eukaryotes.
“many proteins that form complexes in prokaryotes are fused into long, single-chain, multidomain proteins in eukaryotes4.”
From AF2Complex predicts direct physical interactions in multimeric proteins with deep learning (2022) · cites this paper as [4]
The two CcmH domains are an exception to the notion that fused proteins directly interact.
“This is an exception to the notion that fused proteins directly interact4.”
From AF2Complex predicts direct physical interactions in multimeric proteins with deep learning (2022) · cites this paper as [4]
The citation lists haven’t been fetched yet
References 22 · Cited by 1,670
- Authors
- Marcotte, E. M., Pellegrini, M., Ng, H.-L., Rice, D. W., Yeates, T. O., & Eisenberg, D.
- Affiliations
- University of California, Los Angeles (US)
- Corresponding author
- Eisenberg, David
- Venue
- Science
- Published
- 1999-07-30
- Volume
- 285
- Issue
- 5428
- Pages
- 751-753
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2109715166
- Cited by
- 1,670
- References
- 22
- Citations by year
- 2026: 12 · 2025: 18 · 2024: 17 · 2023: 15 · 2022: 31 · 2021: 32 · 2020: 19 · 2019: 39 · 2018: 41 · 2017: 56 · 2016: 35 · 2015: 50 · 2014: 43 · 2013: 56 · 2012: 73
- FWCI
- 28.64
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (P01GM031299, P01 GM 31299)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Keywords
- protein-protein interaction, protein function prediction, homologous proteins, gene fusion, genome sequence analysis, Escherichia coli, yeast, protein complexes, biological pathways
- MeSH terms
- Amino Acid Sequence, Bacterial Proteins, Binding Sites, Escherichia coli, Fungal Proteins, Humans, Models, Biological, Proteins, Sequence Homology, Nucleic Acid, Thermodynamics, Databases, Factual, Genome, Genome, Bacterial, Genome, Fungal, Sequence Homology, Amino Acid, Evolution, Molecular, Computational Biology
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
