ArticleNature methods2019
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold.
Article in Nature methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 210 papers, 1 of them a synthesis that pooled it.
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Who cites it
210 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Advances in the Application of Protein Language Modeling for Nucleic Acid Protein Binding Site Prediction.Genes · 2024Pooled it
- Article
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- Multi-objective antibody design and optimization using machine learning.Nature reviews bioengineering · 2026Article
- SEVA: structural and evolutionary feature integration for predicting virulence factors and antibiotic resistance genes.Microbiome · 2026Article
- Structure-aware artificial intelligence for next-generation drug discovery: from protein-ligand modeling to generative biomolecular design.Briefings in bioinformatics · 2026Review
- Target identification and assessment in the era of AI.Nature reviews. Drug discovery · 2026Review
- Conserved pathway for homarine catabolism in environmental bacteria.Nature microbiology · 2026Article
- Protein foundation models: a comprehensive survey.Science China. Life sciences · 2026Review
- A multi-target drug design method based on target feature fusion.BMC bioinformatics · 2026Article
- Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER.Nature biotechnology · 2026Article
- Clustering the protein universe of life using DIAMOND DeepClust.Nature methods · 2026Article
- CKAN-ATHP: a predictor for antihypertensive peptides based on sample augmentation and loss improvement strategies using the convolutional Kolmogorov-Arnold network.Journal of cheminformatics · 2026Article
- Inferring context-specific site variation with evotuned protein language models.NAR genomics and bioinformatics · 2026Article
- PepScorer::RMSD: An Improved Machine Learning Scoring Function for Protein-Peptide Docking.International journal of molecular sciences · 2026Article
- Root-associated protein prediction using a protein large language model and hypergraph convolutional networks.Scientific reports · 2026Article
- iDLDDG: predicting protein stability changes from missense mutations in DNA-binding proteins using integrated deep learning features.Briefings in bioinformatics · 2026Article
- Enhancing protein immunogenicity prediction via uncertainty weighted deep ensemble.Oxford open immunology · 2026Article
- Improving AlphaFold2- and AlphaFold3-Based Protein Complex Structure Prediction With MULTICOM4 in CASP16.Proteins · 2026Article
150 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The open-source de novo protein-level assembler, Plass ( https://plass.mmseqs.com ), assembles six-frame-translated sequencing reads into protein sequences. It recovers 2-10 times more protein sequences from complex metagenomes and can assemble huge datasets. We assembled two redundancy-filtered reference protein catalogs, 2 billion sequences from 640 soil samples (soil reference protein catalog) and 292 million sequences from 775 marine eukaryotic metatranscriptomes (marine eukaryotic reference catalog), the largest free collections of protein sequences.
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Registered trials
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