ArticleGenome biology2019
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
- Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER.Nature biotechnology · 2026Article
- Improving AlphaFold2- and AlphaFold3-Based Protein Complex Structure Prediction With MULTICOM4 in CASP16.Proteins · 2026Article
- Boosting AlphaFold protein tertiary structure prediction through MSA engineering and extensive model sampling and ranking in CASP16.Communications biology · 2025Article
- Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns.Viruses · 2025Article
- NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation.Nature communications · 2025Article
- Petabase-Scale Homology Search for Structure Prediction.Cold Spring Harbor perspectives in biology · 2024Review
- Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data.Nature methods · 2024Article
- The origin and structural evolution of de novo genes in Drosophila.Nature communications · 2024Article
- Precision enzyme discovery through targeted mining of metagenomic data.Natural products and bioprospecting · 2024Review
- Article
- Petascale Homology Search for Structure Prediction.bioRxiv : the preprint server for biology · 2023Article
- Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship.Communications biology · 2023Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- Contact-Assisted Threading in Low-Homology Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more.Acta crystallographica. Section D, Structural biology · 2022Article
- Ontology-aware deep learning enables ultrafast and interpretable source tracking among sub-million microbial community samples from hundreds of niches.Genome medicine · 2022Article
- Review
- Using metagenomic data to boost protein structure prediction and discovery.Computational and structural biotechnology journal · 2022Review
- Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A roadmap for metagenomic enzyme discovery.Natural product reports · 2021Review
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8 authors.
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Abstract
introductionThe ocean microbiome represents one of the largest microbiomes and produces nearly half of the primary energy on the planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, we explore new applications of oceanic metagenomes for protein structure and function prediction.
resultsBy processing 1.3 TB of high-quality reads from the Tara Oceans data, we obtain 97 million non-redundant genes. Of the 5721 Pfam families that lack experimental structures, 2801 have at least one member associated with the oceanic metagenomics dataset. We apply C-QUARK, a deep-learning contact-guided ab initio structure prediction pipeline, to model 27 families, where 20 are predicted to have a reliable fold with estimated template modeling score (TM-score) at least 0.5. Detailed analyses reveal that the abundance of microbial genera in the ocean is highly correlated to the frequency of occurrence in the modeled Pfam families, suggesting the significant role of the Tara Oceans genomes in the contact-map prediction and subsequent ab initio folding simulations. Of interesting note, PF15461, which has a majority of members coming from ocean-related bacteria, is identified as an important photosynthetic protein by structure-based function annotations. The pipeline is extended to a set of 417 Pfam families, built on the combination of Tara with other metagenomics datasets, which results in 235 families with an estimated TM-score over 0.5.
conclusionsThese results demonstrate a new avenue to improve the capacity of protein structure and function modeling through marine metagenomics, especially for difficult proteins with few homologous sequences.
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