ArticleNucleic acids research2021
PSORTdb 4.0: expanded and redesigned bacterial and archaeal protein subcellular localization database incorporating new secondary localizations.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 41 citations in OpenAlex.
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- Ayu: a machine intelligence tool for identification of extracellular proteins in the marine secretome.Nature communications · 2025Article
- Highly multiplexed spatial transcriptomics in bacteria.Science (New York, N.Y.) · 2025Article
- Biodegradation of ZEN byFrontiers in microbiology · 2025Article
- Serovar-specific genomic features ofFrontiers in molecular biosciences · 2025Article
- Protein subcellular localization prediction tools.Computational and structural biotechnology journal · 2024Review
- Predicting the subcellular location of prokaryotic proteins with DeepLocPro.Bioinformatics (Oxford, England) · 2024Article
- Cellular location shapes quaternary structure of enzymes.Nature communications · 2024Article
- Highly Multiplexed Spatial Transcriptomics in Bacteria.bioRxiv : the preprint server for biology · 2024Article
- RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases.Protein science : a publication of the Protein Society · 2024Article
- Extracellular vesicles from vaginal Gardnerella vaginalis and Mobiluncus mulieris contain distinct proteomic cargo and induce inflammatory pathways.NPJ biofilms and microbiomes · 2024Article
- dbMisLoc: A Manually Curated Database of Conditional Protein Mis-localization Events.Interdisciplinary sciences, computational life sciences · 2023Article
- Molecular dynamics and simulation analysis against superoxide dismutase (SOD) target ofSaudi journal of biological sciences · 2023Article
- Pathogen-associated gene discovery workflows for novel antivirulence therapeutic development.EBioMedicine · 2023Review
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
Protein subcellular localization (SCL) is important for understanding protein function, genome annotation, and aids identification of potential cell surface diagnostic markers, drug targets, or vaccine components. PSORTdb comprises ePSORTdb, a manually curated database of experimentally verified protein SCLs, and cPSORTdb, a pre-computed database of PSORTb-predicted SCLs for NCBI's RefSeq deduced bacterial and archaeal proteomes. We now report PSORTdb 4.0 (http://db.psort.org/). It features a website refresh, in particular a more user-friendly database search. It also addresses the need to uniquely identify proteins from NCBI genomes now that GI numbers have been retired. It further expands both ePSORTdb and cPSORTdb, including additional data about novel secondary localizations, such as proteins found in bacterial outer membrane vesicles. Protein predictions in cPSORTdb have increased along with the number of available microbial genomes, from approximately 13 million when PSORTdb 3.0 was released, to over 66 million currently. Now, analyses of both complete and draft genomes are included. This expanded database will be of wide use to researchers developing SCL predictors or studying diverse microbes, including medically, agriculturally and industrially important species that have both classic or atypical cell envelope structures or vesicles.
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Registered trials
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