ArticleScience (New York, N.Y.)2017
Protein structure determination using metagenome sequence data.
Article in Science (New York, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 244 papers.
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Who cites it
244 citing papers in PubMed.
- Review
- GLMYsymm: inferring symmetry categories of protein complexes from single sequences using persistent GLMY homology.Briefings in bioinformatics · 2026Article
- Energy Landscape Analysis of Membrane Proteins Using NMR-Based Hybrid Restraint Potentials.Journal of chemical theory and computation · 2026Article
- Interpretable machine learning uncovers structural determinants of Wnt-Wntless binding specificity from atomistic simulations.Communications chemistry · 2026Article
- Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER.Nature biotechnology · 2026Article
- Disentangling coevolutionary constraints for modeling protein conformational heterogeneity.Communications chemistry · 2026Article
- 20 Years of the ISCB Student Council Symposium: shaping computational biology and future leaders.Bioinformatics advances · 2026Article
- Mechanism of activation of an ancestral TEC kinase by PIPNpj structural biology · 2026Article
- AI-Driven Protein Research: From Prediction to Design.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Computational design of class II MHC binding peptide with sequence-based evolution information.Bioinformatics advances · 2026Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Alternative Conformation Prediction Using Deep Learning With Multi-MSA Strategy and Structural Clustering in CASP16.Proteins · 2026Article
- Evaluating the significance of embedding-based protein sequence alignment with clustering and double dynamic programming for remote homology.Scientific reports · 2025Article
- Predicting protein-protein interactions in the human proteome.Science (New York, N.Y.) · 2025Article
- The ethics of using artificial intelligence in scientific research: new guidance needed for a new tool.AI and ethics · 2025Article
- The RNA helicase HrpA rescues collided ribosomes in E. coli.Molecular cell · 2025Article
- NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation.Nature communications · 2025Article
- Article
- Exploring Evolution to Uncover Insights Into Protein Mutational Stability.Molecular biology and evolution · 2025Article
- Predicting antibiotic resistance genes and bacterial phenotypes based on protein language models.Frontiers in microbiology · 2025Article
184 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost.
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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.