ArticleNature communications2023
Sequence-structure-function relationships in the microbial protein universe.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
What it found
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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.
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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.
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Who cites it
48 citing papers in PubMed, 95 citations in OpenAlex.
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- A trimodal protein language model enables advanced protein searches.Nature biotechnology · 2026Article
- Bridging Algorithms and Biocatalysis: Perspectives on AI-Supported Enzyme Engineering.Molecules (Basel, Switzerland) · 2026Review
- Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.mSystems · 2026Article
- From Sequence to Solution: Computational Design of a Multi-Epitope Vaccine Candidate Against Francisella tularensis.Probiotics and antimicrobial proteins · 2026Article
- Polarization as a Process: The Potential of Process Ontology for Understanding Cellular Symmetry Breaking.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Deep homology and design of proteasome chaperone proteins in Candidozyma auris.Nature communications · 2026Article
- Analysis of Sequence Diversity in Subfamilies of Phytochrome-Linked Effectors.Methods in molecular biology (Clifton, N.J.) · 2026Article
- BileActome reveals community-assembled bile acid metabolism in the rumen microbiome.ISME communications · 2026Article
- UNKAI: A Protein Functional Identity Prediction Model Based on ESM-C Latent Representations and the Attention Mechanism.Computational and structural biotechnology journal · 2026Article
- Identification and Classification of Fungal GPCR Gene Families.Journal of fungi (Basel, Switzerland) · 2025Article
- Protein language models uncover carbohydrate-active enzyme function in metagenomics.BMC bioinformatics · 2025Article
- Microbial protein-derived bioplastics from renewable substrates: pathways, challenges, and applications in a circular economy.Environmental science and ecotechnology · 2025Review
- Comprehensive Analysis of the ARF Gene Family Reveals Their Roles in Chinese Chestnut (Biology · 2025Article
- DeepSEA: an alignment-free explainable approach to annotate antimicrobial resistance proteins.BMC bioinformatics · 2025Article
- A comprehensive dataset of therapeutic peptides on multi-function property and structure information.Scientific data · 2025Article
- Deep learning-enhanced clustering and classification of protein molecule tertiary structures using weighted distance matrices.Briefings in bioinformatics · 2025Article
- Towards a comprehensive view of the pocketome universe-biological implications and algorithmic challenges.PLoS computational biology · 2025Article
Corrections and comments
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Authors and funding
16 authors at 8 institutions in 6 countries.
Funding
Abstract
For the past half-century, structural biologists relied on the notion that similar protein sequences give rise to similar structures and functions. While this assumption has driven research to explore certain parts of the protein universe, it disregards spaces that don't rely on this assumption. Here we explore areas of the protein universe where similar protein functions can be achieved by different sequences and different structures. We predict ~200,000 structures for diverse protein sequences from 1,003 representative genomes across the microbial tree of life and annotate them functionally on a per-residue basis. Structure prediction is accomplished using the World Community Grid, a large-scale citizen science initiative. The resulting database of structural models is complementary to the AlphaFold database, with regards to domains of life as well as sequence diversity and sequence length. We identify 148 novel folds and describe examples where we map specific functions to structural motifs. We also show that the structural space is continuous and largely saturated, highlighting the need for a shift in focus across all branches of biology, from obtaining structures to putting them into context and from sequence-based to sequence-structure-function based meta-omics analyses.
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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.