ArticleTraffic (Copenhagen, Denmark)2016
Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains.
Article in Traffic (Copenhagen, Denmark), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening.Nature communications · 2024Article
- The GTPase activating protein Gyp7 regulates Rab7/Ypt7 activity on late endosomes.The Journal of cell biology · 2024Article
- Evolutionary history of the cytochrome P450s from Colletotrichum species and prediction of their putative functional roles during host-pathogen interactions.BMC genomics · 2024Article
- Article
- Endoplasmic Reticulum Membrane Contact Sites, Lipid Transport, and Neurodegeneration.Cold Spring Harbor perspectives in biology · 2023Review
- In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms.Proteins · 2023Article
- Pangenome-level analysis of nucleoid-associated proteins in theFrontiers in microbiology · 2023Article
- A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Disease relevance of rare VPS13B missense variants for neurodevelopmental Cohen syndrome.Scientific reports · 2022Article
- Structural and biochemical insights into lipid transport by VPS13 proteins.The Journal of cell biology · 2022Article
- Sequence Analysis and Structural Predictions of Lipid Transfer Bridges in the Repeating Beta Groove (RBG) Superfamily Reveal Past and Present Domain Variations Affecting Form, Function and Interactions of VPS13, ATG2, SHIP164, Hobbit and Tweek.Contact (Thousand Oaks (Ventura County, Calif.)) · 2022Article
- Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities.Frontiers in microbiology · 2022Article
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- Identification and functional characterization ofFrontiers in microbiology · 2022Article
- The GTPase Arf1 Is a Determinant of Yeast Vps13 Localization to the Golgi Apparatus.International journal of molecular sciences · 2021Article
- COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets.Briefings in bioinformatics · 2021Article
- Mapping the glycosyltransferase fold landscape using interpretable deep learning.Nature communications · 2021Article
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7 authors.
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Abstract
Advances in membrane cell biology are hampered by the relatively high proportion of proteins with no known function. Such proteins are largely or entirely devoid of structurally significant domain annotations. Structural bioinformaticians have developed profile-profile tools such as HHsearch (online version called HHpred), which can detect remote homologies that are missed by tools used to annotate databases. Here we have applied HHsearch to study a single structural fold in a single model organism as proof of principle. In the entire clan of protein domains sharing the pleckstrin homology domain fold in yeast, systematic application of HHsearch accurately identified known PH-like domains. It also predicted 16 new domains in 13 yeast proteins many of which are implicated in intracellular traffic. One of these was Vps13p, where we confirmed the functional importance of the predicted PH-like domain. Even though such predictions require considerable work to be corroborated, they are useful first steps. HHsearch should be applied more widely, particularly across entire proteomes of model organisms, to significantly improve database annotations.
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