ArticleNature methods2018
PDB-wide identification of biological assemblies from conserved quaternary structure geometry.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- 3DSeqCheck: A Web-based Tool for Verifying Sequence Consistency Between a 3D Structure File and the Corresponding UniProt Entry.Journal of molecular biology · 2026Article
- Protein Self-Interaction in Cellular Function and Network Evolution: Molecular Mechanisms, AI-Driven Insights, and Therapeutic Potentials.International journal of molecular sciences · 2026Review
- The microbiome regulates host metabolic health and diseases through microbial enzymes.Nature reviews. Gastroenterology & hepatology · 2026Review
- Reciprocal best matching: a new pipeline for scoring models with unknown stoichiometry in CASP experiments.BMC bioinformatics · 2026Article
- QSProteome: a community-driven interactive platform for large-scale exploration and evaluation of predicted protein complex structures.Nucleic acids research · 2026Article
- Comprehensive Pan-Cancer Analysis Reveals RNF20 as a Candidate Prognostic and Diagnostic Biomarker.Bioinformatics and biology insights · 2026Article
- A new age in structural S-layer biology: Experimental and in silico milestones.The Journal of biological chemistry · 2025Review
- Rapid and sensitive protein complex alignment with Foldseek-Multimer.Nature methods · 2025Article
- Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm.Nature communications · 2025Article
- Exploring Shootin1's oncogenic role withinTurkish journal of biology = Turk biyoloji dergisi · 2025Article
- Frequent transitions in self-assembly across the evolution of a central metabolic enzyme.Nature communications · 2024Article
- Frequent transitions in self-assembly across the evolution of a central metabolic enzyme.bioRxiv : the preprint server for biology · 2024Article
- A suite of designed protein cages using machine learning and protein fragment-based protocols.Structure (London, England : 1993) · 2024Article
- Mutational biases favor complexity increases in protein interaction networks after gene duplication.Molecular systems biology · 2024Article
- Rapid and accurate prediction of protein homo-oligomer symmetry with Seq2Symm.Research square · 2024Article
- Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data.Scientific data · 2023Article
- Protein language models can capture protein quaternary state.BMC bioinformatics · 2023Article
- A Suite of Designed Protein Cages Using Machine Learning Algorithms and Protein Fragment-Based Protocols.bioRxiv : the preprint server for biology · 2023Article
- Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.Proteomics · 2023Article
- The protein common assembly database (ProtCAD)-a comprehensive structural resource of protein complexes.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein structures are key to understanding biomolecular mechanisms and diseases, yet their interpretation is hampered by limited knowledge of their biologically relevant quaternary structure (QS). A critical challenge in inferring QS information from crystallographic data is distinguishing biological interfaces from fortuitous crystal-packing contacts. Here, we tackled this problem by developing strategies for aligning and comparing QS states across both homologs and data repositories. QS conservation across homologs proved remarkably strong at predicting biological relevance and is implemented in two methods, QSalign and anti-QSalign, for annotating homo-oligomers and monomers, respectively. QS conservation across repositories is implemented in QSbio (http://www.QSbio.org), which approaches the accuracy of manual curation and allowed us to predict >100,000 QS states across the Protein Data Bank. Based on this high-quality data set, we analyzed pairs of structurally conserved interfaces, and this analysis revealed a striking plasticity whereby evolutionary distant interfaces maintain similar interaction geometries through widely divergent chemical properties.
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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.