ArticleBMC bioinformatics2009
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers.
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141 citing papers in PubMed.
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- RSLpred2: An Integrated Web Server for the Annotation of Rice Proteome Subcellular Localization Using Deep Learning.Rice (New York, N.Y.) · 2025Article
- Chromosome-Level Assemblies of the Allohexaploid Genomes of Conyza sumatrensis and Conyza bonariensis.Genome biology and evolution · 2025Article
- Deep generative model for protein subcellular localization prediction.Briefings in bioinformatics · 2025Article
- Application of integrated omics in aseptic loosening of prostheses after hip replacement.Molecular medicine reports · 2025Article
- AtSubP-2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning.The plant genome · 2025Article
- Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region.The Plant journal : for cell and molecular biology · 2025Article
- Article
- OsAPSE modulates non-covalent interactions between arabinogalactan proteinFrontiers in plant science · 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
- Comprehensive Transcriptome and Proteome Analyses Reveal the Drought Responsive Gene Network in Potato Roots.Plants (Basel, Switzerland) · 2024Article
- SCLpred-ECL: Subcellular Localization Prediction by Deep N-to-1 Convolutional Neural Networks.International journal of molecular sciences · 2024Article
- Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment.Nucleic acids research · 2024Article
- Predictive Modeling of Proteins Encoded by a Plant Virus Sheds a New Light on Their Structure and Inherent Multifunctionality.Biomolecules · 2024Article
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Abstract
backgroundKnowledge of subcellular localization of proteins is crucial to proteomics, drug target discovery and systems biology since localization and biological function are highly correlated. In recent years, numerous computational prediction methods have been developed. Nevertheless, there is still a need for prediction methods that show more robustness and higher accuracy.
resultsWe extended our previous MultiLoc predictor by incorporating phylogenetic profiles and Gene Ontology terms. Two different datasets were used for training the system, resulting in two versions of this high-accuracy prediction method. One version is specialized for globular proteins and predicts up to five localizations, whereas a second version covers all eleven main eukaryotic subcellular localizations. In a benchmark study with five localizations, MultiLoc2 performs considerably better than other methods for animal and plant proteins and comparably for fungal proteins. Furthermore, MultiLoc2 performs clearly better when using a second dataset that extends the benchmark study to all eleven main eukaryotic subcellular localizations.
conclusionMultiLoc2 is an extensive high-performance subcellular protein localization prediction system. By incorporating phylogenetic profiles and Gene Ontology terms MultiLoc2 yields higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. MultiLoc2 is available as user-friendly and free web-service, available at: http://www-bs.informatik.uni-tuebingen.de/Services/MultiLoc2.
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