ArticleStructure (London, England : 1993)2010
Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification.
Article in Structure (London, England : 1993), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution.Genome research · 2026Article
- CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models.Bioinformatics (Oxford, England) · 2023Article
- Creative destruction: New protein folds from old.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Structural dynamics in the evolution of a bilobed protein scaffold.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds.Frontiers in molecular biosciences · 2021Review
- Review
- Diversity in protein domain superfamilies.Current opinion in genetics & development · 2015Review
- Domain atrophy creates rare cases of functional partial protein domains.Genome biology · 2015Article
- Article
- LenVarDB: database of length-variant protein domains.Nucleic acids research · 2014Article
- ThreaDom: extracting protein domain boundary information from multiple threading alignments.Bioinformatics (Oxford, England) · 2013Article
- Functional site plasticity in domain superfamilies.Biochimica et biophysica acta · 2013Article
- Article
- p42.3 gene expression in gastric cancer cell and its protein regulatory network analysis.Theoretical biology & medical modelling · 2012Article
- Article
- A large conformational change in the putative ATP pyrophosphatase PF0828 induced by ATP binding.Acta crystallographica. Section F, Structural biology and crystallization communications · 2011Article
- Metagenomics and the protein universe.Current opinion in structural biology · 2011Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Some superfamilies contain large numbers of protein domains with very different functions. The ability to refine the functional classification of domains within these superfamilies is necessary for better understanding the evolution of functions and to guide function prediction of new relatives. To achieve this, a suitable starting point is the detailed analysis of functional divisions and mechanisms of functional divergence in a single superfamily. Here, we present such a detailed analysis in the superfamily of HUP domains. A biologically meaningful functional classification of HUP domains is obtained manually. Mechanisms of function diversification are investigated in detail using this classification. We observe that structural motifs play an important role in shaping broad functional divergence, whereas residue-level changes shape diversity at a more specific level. In parallel we examine the ability of an automated protocol to capture the biologically meaningful classification, with a view to automatically extending this classification in the future.
Indexed as
Identifiers
What OpenQuestion holds
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.