ArticleProceedings of the National Academy of Sciences of the United States of America2017
Origins of coevolution between residues distant in protein 3D structures.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
100 citing papers in PubMed, 212 citations in OpenAlex.
- Graph-based representations in modern protein science.The Biochemical journal · 2026Review
- Disentangling coevolutionary constraints for modeling protein conformational heterogeneity.Communications chemistry · 2026Article
- From single-sequences to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2.Nature communications · 2026Article
- Article
- Stable de novo protein design via joint conformational landscape and sequence optimization.Nature communications · 2025Article
- Modeling the structure-conditioned sequence landscape for large-scale protein design with TriFlow.bioRxiv : the preprint server for biology · 2025Article
- Protein design drives synthetic biology research of plant natural products.Biodesign research · 2025Review
- Exploring the origins of a signaling pathway.eLife · 2025Article
- Molecular contacts in self-assembling clusters of membrane proteins.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- PHACE: Phylogeny-Aware Detection of Molecular Coevolution.Molecular biology and evolution · 2025Article
- Influence of mutations at different distances from the active center on the activity and stability of laccase 13B22.Bioresources and bioprocessing · 2025Article
- Recent progress and future challenges in structure-based protein-protein interaction prediction.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Emerging frontiers in protein structure prediction following the AlphaFold revolution.Journal of the Royal Society, Interface · 2025Review
- Identification of coevolving positions by ancestral reconstruction.Communications biology · 2025Article
- MetalNet2: an enhanced server for predicting metal-binding sites in proteomes.National science review · 2024Article
- Structure prediction of alternative protein conformations.Nature communications · 2024Article
- Accurate prediction of protein function using statistics-informed graph networks.Nature communications · 2024Article
- Molecular characterization of Rft1, an ER membrane protein associated with congenital disorder of glycosylation RFT1-CDG.bioRxiv : the preprint server for biology · 2024Article
- Metamorphic proteins and how to find them.Current opinion in structural biology · 2024Review
- Engineering Proteins Using Statistical Models of Coevolutionary Sequence Information.Cold Spring Harbor perspectives in biology · 2024Review
40 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Residue pairs that directly coevolve in protein families are generally close in protein 3D structures. Here we study the exceptions to this general trend-directly coevolving residue pairs that are distant in protein structures-to determine the origins of evolutionary pressure on spatially distant residues and to understand the sources of error in contact-based structure prediction. Over a set of 4,000 protein families, we find that 25% of directly coevolving residue pairs are separated by more than 5 Å in protein structures and 3% by more than 15 Å. The majority (91%) of directly coevolving residue pairs in the 5-15 Å range are found to be in contact in at least one homologous structure-these exceptions arise from structural variation in the family in the region containing the residues. Thirty-five percent of the exceptions greater than 15 Å are at homo-oligomeric interfaces, 19% arise from family structural variation, and 27% are in repeat proteins likely reflecting alignment errors. Of the remaining long-range exceptions (<1% of the total number of coupled pairs), many can be attributed to close interactions in an oligomeric state. Overall, the results suggest that directly coevolving residue pairs not in repeat proteins are spatially proximal in at least one biologically relevant protein conformation within the family; we find little evidence for direct coupling between residues at spatially separated allosteric and functional sites or for increased direct coupling between residue pairs on putative allosteric pathways connecting them.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.