ArticleEntropy (Basel, Switzerland)2020
Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting.
Article in Entropy (Basel, Switzerland), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Impact of phylogeny on the inference of functional sectors from protein sequence data.PLoS computational biology · 2024Article
- Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies.Biophysical journal · 2024Article
- Article
- Data-driven design of orthogonal protein-protein interactions.Science signaling · 2023Article
- Impact of phylogeny on structural contact inference from protein sequence data.Journal of the Royal Society, Interface · 2023Article
- Protein language models trained on multiple sequence alignments learn phylogenetic relationships.Nature communications · 2022Article
- Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences.PLoS computational biology · 2022Article
- Extracting phylogenetic dimensions of coevolution reveals hidden functional signals.Scientific reports · 2022Article
- Information Theory in Molecular Evolution: From Models to Structures and Dynamics.Entropy (Basel, Switzerland) · 2021Article
- Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention.Pacific Symposium on Biocomputing. Pacific Symposium on BiocomputingArticle
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2 authors.
Funding
Abstract
Extracting structural information from sequence co-variation has become a common computational biology practice in the recent years, mainly due to the availability of large sequence alignments of protein families. However, identifying features that are specific to sub-classes and not shared by all members of the family using sequence-based approaches has remained an elusive problem. We here present a coevolutionary-based method to differentially analyze subfamily specific structural features by a continuous sequence reweighting (SR) approach. We introduce the underlying principles and test its predictive capabilities on the Response Regulator family, whose subfamilies have been previously shown to display distinct, specific homo-dimerization patterns. Our results show that this reweighting scheme is effective in assigning structural features known a priori to subfamilies, even when sequence data is relatively scarce. Furthermore, sequence reweighting allows assessing if individual structural contacts pertain to specific subfamilies and it thus paves the way for the identification specificity-determining contacts from sequence variation data.
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