ArticleNucleic acids research2016
PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers, 1 of them a synthesis that pooled it.
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Who cites it
47 citing papers in PubMed, 1 synthesis or guideline pooled it, 85 citations in OpenAlex.
- Pooled it
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- A review from biological mapping to computation-based subcellular localization.Molecular therapy. Nucleic acids · 2023Review
- A simple and efficient fluorescent labeling method inFrontiers in microbiology · 2023Article
- Bacterial Outer Membrane Polysaccharide Export (OPX) Proteins Occupy Three Structural Classes with Selective β-Barrel Porin Requirements for Polymer Secretion.Microbiology spectrum · 2022Article
- Interaction between transcribing RNA polymerase and topoisomerase I prevents R-loop formation in E. coli.Nature communications · 2022Article
- Antioxidants of Fruit Extracts as Antimicrobial Agents against Pathogenic Bacteria.Antioxidants (Basel, Switzerland) · 2022Review
- Designing of a Recombinant Multi-Epitopes Based Vaccine againstInternational journal of environmental research and public health · 2022Article
- Functional Annotation of Hypothetical Proteins From theBioinformatics and biology insights · 2022Article
- Article
- Adaptation to Varying Salinity inFrontiers in microbiology · 2022Article
- Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups.The ISME journal · 2022Article
- Computational design and characterization of a multiepitope vaccine against carbapenemase-producingComputational and structural biotechnology journal · 2022Article
- PSORTdb 4.0: expanded and redesigned bacterial and archaeal protein subcellular localization database incorporating new secondary localizations.Nucleic acids research · 2021Article
- Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior.Nucleic acids research · 2021Article
- Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions.Frontiers in microbiology · 2021Review
- OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins.Frontiers in bioinformatics · 2021Article
- Comparative population genomic analyses of transporters within the Asgard archaeal superphylum.PloS one · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein subcellular localization (SCL) is important for understanding protein function, genome annotation, and has practical applications such as identification of potential vaccine components or diagnostic/drug targets. PSORTdb (http://db.psort.org) comprises manually curated SCLs for proteins which have been experimentally verified (ePSORTdb), as well as pre-computed SCL predictions for deduced proteomes from bacterial and archaeal complete genomes available from NCBI (cPSORTdb). We now report PSORTdb 3.0. It features improvements increasing user-friendliness, and further expands both ePSORTdb and cPSORTdb with a focus on improving protein SCL data in cases where it is most difficult-proteins associated with non-classical Gram-positive/Gram-negative/Gram-variable cell envelopes. ePSORTdb data curation was expanded, including adding in additional cell envelope localizations, and incorporating markers for cPSORTdb to automatically computationally identify if new genomes to be analysed fall into certain atypical cell envelope categories (i.e. Deinococcus-Thermus, Thermotogae, Corynebacteriales/Corynebacterineae, including Mycobacteria). The number of predicted proteins in cPSORTdb has increased from 3,700,000 when PSORTdb 2.0 was released to over 13,000,000 currently. PSORTdb 3.0 will be of wider use to researchers studying a greater diversity of monoderm or diderm microbes, including medically, agriculturally and industrially important species that have non-classical outer membranes or other cell envelope features.
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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.