ArticlePLoS computational biology2014
NESmapper: accurate prediction of leucine-rich nuclear export signals using activity-based profiles.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 51 citations in OpenAlex.
- FgNup2 regulates nuclear import of the histone H2B monoubiquitination enzyme by stabilizing the FgImpα-FgBre1 complex to mediate pathogenicity in Fusarium graminearum.PLoS pathogens · 2026Article
- SPSignal: a web tool for structure-assisted prediction of nuclear localization and nuclear export signals in proteins.Nucleic acids research · 2026Article
- Multiple roads between the nucleus and the cytoplasm: classes of linear NLSs and NESs and their receptors.Current opinion in structural biology · 2026Review
- Nuclear-Cytoplasmic Axis in Cancer: From Protein Mislocalization to Anticancer Drug Resistance.Oncology research · 2026Review
- The nuclear export receptor CRM1/XPO1 and its diverse cargoes.Trends in biochemical sciences · 2025Review
- The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.Molecular cell · 2025Article
- MULoc-target: Targeting peptide classification and detection using a protein language model.Briefings in bioinformatics · 2025Article
- Phosphate-dependent nuclear export via a non-classical NES class recognized by exportin Msn5.Nature communications · 2025Article
- Defining ortholog-specific UHRF1 inhibition by STELLA for cancer therapy.Nature communications · 2025Article
- TIRR regulates mRNA export and association with P-bodies in response to DNA damage.Nucleic acids research · 2024Article
- Target gene responses differ when transcription factor levels are acutely decreased by nuclear export versus degradation.Development (Cambridge, England) · 2024Article
- Target gene responses differ when transcription factor levels are acutely decreased by nuclear export versus degradation.bioRxiv : the preprint server for biology · 2024Article
- Phylogenomics analysis of velvet regulators in the fungal kingdom.Microbiology spectrum · 2024Article
- Alternative splicing of HDAC7 regulates its interaction with 14-3-3 proteins to alter histone marks and target gene expression.Cell reports · 2023Article
- Identification of phosphorylation site on PARP1 mediating its cytosolic translocation in virus-infected HeLa cells.STAR protocols · 2022Article
- The superior salinity tolerance of bread wheat cultivar Shanrong No. 3 is unlikely to be caused by elevated Ta-sro1 poly-(ADP-ribose) polymerase activity.The Plant cell · 2022Article
- Karyopherin-mediated nucleocytoplasmic transport.Nature reviews. Molecular cell biology · 2022Review
- Nuclear dynamics: Formation of bodies and trafficking in plant nuclei.Frontiers in plant science · 2022Review
- Characterization of Localization and Export Signals of Bovine Torovirus Nucleocapsid Protein Responsible for Extensive Nuclear and Nucleolar Accumulation and Their Importance for Virus Growth.Journal of virology · 2021Article
- Nuclear Exportin 1 (XPO1) Binds to the Nuclear Localization/Export Signal of the Turnip Mosaic Virus NIb to Promote Viral Infection.Frontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The nuclear export of proteins is regulated largely through the exportin/CRM1 pathway, which involves the specific recognition of leucine-rich nuclear export signals (NESs) in the cargo proteins, and modulates nuclear-cytoplasmic protein shuttling by antagonizing the nuclear import activity mediated by importins and the nuclear import signal (NLS). Although the prediction of NESs can help to define proteins that undergo regulated nuclear export, current methods of predicting NESs, including computational tools and consensus-sequence-based searches, have limited accuracy, especially in terms of their specificity. We found that each residue within an NES largely contributes independently and additively to the entire nuclear export activity. We created activity-based profiles of all classes of NESs with a comprehensive mutational analysis in mammalian cells. The profiles highlight a number of specific activity-affecting residues not only at the conserved hydrophobic positions but also in the linker and flanking regions. We then developed a computational tool, NESmapper, to predict NESs by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. This tool successfully reduced the considerable number of false positives, and the overall prediction accuracy was higher than that of other methods, including NESsential and Wregex. This profile-based prediction strategy is a reliable way to identify functional protein motifs. NESmapper is available at http://sourceforge.net/projects/nesmapper.
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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.