ArticleBioinformatics (Oxford, England)2012
LocTree2 predicts localization for all domains of life.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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- Protein subcellular localization prediction tools.Computational and structural biotechnology journal · 2024Review
- Predicting the subcellular location of prokaryotic proteins with DeepLocPro.Bioinformatics (Oxford, England) · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- SCLpred-ECL: Subcellular Localization Prediction by Deep N-to-1 Convolutional Neural Networks.International journal of molecular sciences · 2024Article
- Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Protein Sorting Prediction.Methods in molecular biology (Clifton, N.J.) · 2024Article
- ProtPlat: an efficient pre-training platform for protein classification based on FastText.BMC bioinformatics · 2022Article
- Understanding Diversity, Evolution, and Structure of Small Heat Shock Proteins in Annelida Through in Silico Analyses.Frontiers in physiology · 2022Article
- Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species.Journal of molecular evolution · 2021Article
- Advances and perspectives in discovery and functional analysis of small secreted proteins in plants.Horticulture research · 2021Review
- Evidence for a synergistic effect of post-translational modifications and genomic composition of eEF-1α on the adaptation ofEcology and evolution · 2021Article
- Computational evaluation of anticipated PE_PGRS39 protein involvement in host-pathogen interplay and its integration into vaccine development.3 Biotech · 2021Article
- Bioinformatics: new tools and applications in life science and personalized medicine.Applied microbiology and biotechnology · 2021Review
- Multi-responses of O-methyltransferase genes to salt stress and fiber development of Gossypium species.BMC plant biology · 2021Article
- Computational methods for protein localization prediction.Computational and structural biotechnology journal · 2021Review
- Light attention predicts protein location from the language of life.Bioinformatics advances · 2021Article
- Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences.Frontiers in genetics · 2020Review
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationSubcellular localization is one aspect of protein function. Despite advances in high-throughput imaging, localization maps remain incomplete. Several methods accurately predict localization, but many challenges remain to be tackled.
resultsIn this study, we introduced a framework to predict localization in life's three domains, including globular and membrane proteins (3 classes for archaea; 6 for bacteria and 18 for eukaryota). The resulting method, LocTree2, works well even for protein fragments. It uses a hierarchical system of support vector machines that imitates the cascading mechanism of cellular sorting. The method reaches high levels of sustained performance (eukaryota: Q18=65%, bacteria: Q6=84%). LocTree2 also accurately distinguishes membrane and non-membrane proteins. In our hands, it compared favorably with top methods when tested on new data. AVAILABILITY: Online through PredictProtein (predictprotein.org); as standalone version at http://www.rostlab.org/services/loctree2. CONTACT: localization@rostlab.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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