ArticleScience advances2017
An ambiguity principle for assigning protein structural domains.
Article in Science advances, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Family-level specialization in protein domain insertion architectures.Protein science : a publication of the Protein Society · 2026Article
- CASP16 Protein Monomer Structure Prediction Assessment.Proteins · 2026Article
- AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures.Bioinformatics (Oxford, England) · 2025Article
- Foldclass and Merizo-search: scalable structural similarity search for single- and multi-domain proteins using geometric learning.Bioinformatics (Oxford, England) · 2025Article
- Semi-supervised segmentation of RNA 3D structures using density-based clustering.Computational and structural biotechnology journal · 2025Article
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- Hierarchical Analysis of Protein Structures: From Secondary Structures to Protein Units and Domains.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Deep learning for the PSIPRED Protein Analysis Workbench.Nucleic acids research · 2024Article
- Chainsaw: protein domain segmentation with fully convolutional neural networks.Bioinformatics (Oxford, England) · 2024Article
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- ATLAS: protein flexibility description from atomistic molecular dynamics simulations.Nucleic acids research · 2024Article
- Merizo: a rapid and accurate protein domain segmentation method using invariant point attention.Nature communications · 2023Article
- To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units.Proteins · 2023Article
- ICARUS: flexible protein structural alignment based on Protein Units.Bioinformatics (Oxford, England) · 2023Article
- DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria.Nucleic acids research · 2023Article
- A unified approach to protein domain parsing with inter-residue distance matrix.Bioinformatics (Oxford, England) · 2023Article
- Approaches for the Identification of Intrinsically Disordered Protein Domains.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Assignment of structural domains in proteins using diffusion kernels on graphs.BMC bioinformatics · 2022Article
- Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly.Nature communications · 2022Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ambiguity is the quality of being open to several interpretations. For an image, it arises when the contained elements can be delimited in two or more distinct ways, which may cause confusion. We postulate that it also applies to the analysis of protein three-dimensional structure, which consists in dividing the molecule into subunits called domains. Because different definitions of what constitutes a domain can be used to partition a given structure, the same protein may have different but equally valid domain annotations. However, knowledge and experience generally displace our ability to accept more than one way to decompose the structure of an object-in this case, a protein. This human bias in structure analysis is particularly harmful because it leads to ignoring potential avenues of research. We present an automated method capable of producing multiple alternative decompositions of protein structure (web server and source code available at www.dsimb.inserm.fr/sword/). Our innovative algorithm assigns structural domains through the hierarchical merging of protein units, which are evolutionarily preserved substructures that describe protein architecture at an intermediate level, between domain and secondary structure. To validate the use of these protein units for decomposing protein structures into domains, we set up an extensive benchmark made of expert annotations of structural domains and including state-of-the-art domain parsing algorithms. The relevance of our "multipartitioning" approach is shown through numerous examples of applications covering protein function, evolution, folding, and structure prediction. Finally, we introduce a measure for the structural ambiguity of protein molecules.
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