ArticleeLife2015
Large-scale determination of previously unsolved protein structures using evolutionary information.
Article in eLife, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 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.
The trial behind it
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
133 citing papers in PubMed.
- YeiE regulates YeiH to implement sulfite stress resistance inJournal of bacteriology · 2026Article
- A combinatorial mutational map of active non-native protein kinases by deep learning guided sequence design.bioRxiv : the preprint server for biology · 2025Article
- Review
- Combined Computational-Biochemical Approach Offers an Accelerated Path to Membrane Protein Solubilization.Journal of chemical information and modeling · 2023Article
- Learning sequence, structure, and function representations of proteins with language models.bioRxiv : the preprint server for biology · 2023Article
- Enantioselectivity in the enzymatic dehydration of malate and tartrate: Mirror image specificities of structurally similar dehydratases.Protein science : a publication of the Protein Society · 2023Article
- Insights into DNA cleavage by MutL homologs from analysis of conserved motifs in eukaryotic Mlh1.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2023Article
- Evolution of the Immunoglobulin Isotypes-Variations of Biophysical Properties among Animal Classes.Biomolecules · 2023Article
- SARS-CoV2 billion-compound docking.Scientific data · 2023Article
- Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter.Nature communications · 2023Article
- Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data.bioRxiv : the preprint server for biology · 2023Article
- Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications.Computational and structural biotechnology journal · 2023Review
- Development of anti-PD-L1 antibody based on structure prediction of AlphaFold2.Frontiers in immunology · 2023Article
- Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins.The journal of physical chemistry. B · 2022Article
- Modeling of protein conformational changes with Rosetta guided by limited experimental data.Structure (London, England : 1993) · 2022Article
- Mycobacterium tuberculosis encodes a YhhN family membrane protein with lysoplasmalogenase activity that protects against toxic host lysolipids.The Journal of biological chemistry · 2022Article
- Sampling alternative conformational states of transporters and receptors with AlphaFold2.eLife · 2022Article
- Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis.Proteins · 2022Article
- Recruitment of the TolA Protein to Cell Constriction Sites in Escherichia coli via Three Separate Mechanisms, and a Critical Role for FtsWI Activity in Recruitment of both TolA and TolQ.Journal of bacteriology · 2022Article
73 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test of protein structure prediction methods by incorporating residue-residue co-evolution information in the Rosetta structure prediction program. We then describe the use of this method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three-dimensional structures are not available. These models, which are posted online for public access, provide structural information for the over 400,000 proteins belonging to the 58 families and suggest hypotheses about mechanism for the subset for which the function is known, and hypotheses about function for the remainder.
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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.