ArticlePloS one2011
Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
102 citing papers in PubMed.
- NRB-FusePS: A Protein Language Model-Based Multimodal Framework for Predicting Ligand-Binding Residues in Nuclear Receptors.The protein journal · 2026Article
- Genome-wide identification and expression analysis of stress-associated proteins (SAPs) containing A20/AN1 Zinc finger in Dendrobium officinale.BMC plant biology · 2026Article
- Pre-meiotic H1.1 degradation is essential for Arabidopsis gametogenesis.The EMBO journal · 2026Article
- Computational Pipelines for Protein Ubiquitylation Analysis and Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Prediction and analysis of anti-aging peptides using data augmentation and machine learning algorithms.BMC biology · 2025Article
- EUP: Enhanced cross-species prediction of ubiquitination sites via a conditional variational autoencoder network based on ESM2.PLoS computational biology · 2025Article
- AMPGen: an evolutionary information-reserved and diffusion-driven generative model for de novo design of antimicrobial peptides.Communications biology · 2025Article
- Ubigo-X: Protein ubiquitination site prediction using ensemble learning with image-based feature representation and weighted voting.Computational and structural biotechnology journal · 2025Article
- ResUbiNet: A Novel Deep Learning Architecture for Ubiquitination Site Prediction.Current genomics · 2025Article
- AntiBinder: utilizing bidirectional attention and hybrid encoding for precise antibody-antigen interaction prediction.Briefings in bioinformatics · 2024Article
- MLAFP-XN: Leveraging neural network model for development of antifungal peptide identification tool.Heliyon · 2024Article
- HemoFuse: multi-feature fusion based on multi-head cross-attention for identification of hemolytic peptides.Scientific reports · 2024Article
- Prediction of leukemia peptides using convolutional neural network and protein compositions.BMC cancer · 2024Article
- MRM-BERT: a novel deep neural network predictor of multiple RNA modifications by fusing BERT representation and sequence features.RNA biology · 2024Article
- Investigating the Precise Identification of Citrullination Sites with High- Performance Score Metrics Using a Powerful Computation Predicting Tool.Combinatorial chemistry & high throughput screening · 2024Article
- UBE2O reduces the effectiveness of interferon-α via degradation of IFIT3 in hepatocellular carcinoma.Cell death & disease · 2023Article
- Neuronal-specific TNFAIP1 ablation attenuates postoperative cognitive dysfunction via targeting SNAP25 for K48-linked ubiquitination.Cell communication and signaling : CCS · 2023Article
- A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction.Genomics, proteomics & bioinformatics · 2023Review
- SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data.NAR genomics and bioinformatics · 2023Article
- A novel protein encoded by circVPS13D attenuates antiviral innate immunity by targeting MAVS in teleost fish.Journal of virology · 2023Article
42 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As one of the most important reversible protein post-translation modifications, ubiquitination has been reported to be involved in lots of biological processes and closely implicated with various diseases. To fully decipher the molecular mechanisms of ubiquitination-related biological processes, an initial but crucial step is the recognition of ubiquitylated substrates and the corresponding ubiquitination sites. Here, a new bioinformatics tool named CKSAAP_UbSite was developed to predict ubiquitination sites from protein sequences. With the assistance of Support Vector Machine (SVM), the highlight of CKSAAP_UbSite is to employ the composition of k-spaced amino acid pairs surrounding a query site (i.e. any lysine in a query sequence) as input. When trained and tested in the dataset of yeast ubiquitination sites (Radivojac et al, Proteins, 2010, 78: 365-380), a 100-fold cross-validation on a 1∶1 ratio of positive and negative samples revealed that the accuracy and MCC of CKSAAP_UbSite reached 73.40% and 0.4694, respectively. The proposed CKSAAP_UbSite has also been intensively benchmarked to exhibit better performance than some existing predictors, suggesting that it can be served as a useful tool to the community. Currently, CKSAAP_UbSite is freely accessible at http://protein.cau.edu.cn/cksaap_ubsite/. Moreover, we also found that the sequence patterns around ubiquitination sites are not conserved across different species. To ensure a reasonable prediction performance, the application of the current CKSAAP_UbSite should be limited to the proteome of yeast.
Indexed as
Identifiers
What OpenQuestion holds
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.