ArticlePloS one2012
GPS-ARM: computational analysis of the APC/C recognition motif by predicting D-boxes and KEN-boxes.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 51 citations in OpenAlex.
- KSDiffusion: conditional diffusion for kinase-specific phosphorylation site prediction under data-limited and imbalanced regimes.Briefings in bioinformatics · 2026Article
- Notch controls APC/CScience advances · 2025Article
- A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction.Genomics, proteomics & bioinformatics · 2023Review
- GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins.Nucleic acids research · 2023Article
- Counting Degrons: Lessons From Multivalent Substrates for Targeted Protein Degradation.Frontiers in physiology · 2022Review
- Article
- pCysMod: Prediction of Multiple Cysteine Modifications Based on Deep Learning Framework.Frontiers in cell and developmental biology · 2021Article
- MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization.Nucleic acids research · 2020Article
- Kaposi's Sarcoma-Associated Herpesvirus Lytic Replication Is Independent of Anaphase-Promoting Complex Activity.Journal of virology · 2020Article
- GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins.Genomics, proteomics & bioinformatics · 2020Article
- Checkpoint Regulation of Nuclear Tos4 Defines S Phase Arrest in Fission Yeast.G3 (Bethesda, Md.) · 2020Article
- Differential Expression of Genes for Ubiquitin Ligases in Medulloblastoma Subtypes.Cerebellum (London, England) · 2019Article
- SWITCH 1/DYAD is a WINGS APART-LIKE antagonist that maintains sister chromatid cohesion in meiosis.Nature communications · 2019Article
- Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer.Frontiers in genetics · 2019Article
- Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in theProceedings of the National Academy of Sciences of the United States of America · 2017Article
- Determinants and Regulation of Protein Turnover in Yeast.Cell systems · 2017Article
- New Functions of APC/C Ubiquitin Ligase in the Nervous System and Its Role in Alzheimer's Disease.International journal of molecular sciences · 2017Review
- GPS-PAIL: prediction of lysine acetyltransferase-specific modification sites from protein sequences.Scientific reports · 2016Article
- MHC class I-associated peptides derive from selective regions of the human genome.The Journal of clinical investigation · 2016Article
- A genome-scale CRISPR-Cas9 screening method for protein stability reveals novel regulators of Cdc25A.Cell discovery · 2016Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase incorporated with Cdh1 and/or Cdc20 recognizes and interacts with specific substrates, and faithfully orchestrates the proper cell cycle events by targeting proteins for proteasomal degradation. Experimental identification of APC/C substrates is largely dependent on the discovery of APC/C recognition motifs, e.g., the D-box and KEN-box. Although a number of either stringent or loosely defined motifs proposed, these motif patterns are only of limited use due to their insufficient powers of prediction. We report the development of a novel GPS-ARM software package which is useful for the prediction of D-boxes and KEN-boxes in proteins. Using experimentally identified D-boxes and KEN-boxes as the training data sets, a previously developed GPS (Group-based Prediction System) algorithm was adopted. By extensive evaluation and comparison, the GPS-ARM performance was found to be much better than the one using simple motifs. With this powerful tool, we predicted 4,841 potential D-boxes in 3,832 proteins and 1,632 potential KEN-boxes in 1,403 proteins from H. sapiens, while further statistical analysis suggested that both the D-box and KEN-box proteins are involved in a broad spectrum of biological processes beyond the cell cycle. In addition, with the co-localization information, we predicted hundreds of mitosis-specific APC/C substrates with high confidence. As the first computational tool for the prediction of APC/C-mediated degradation, GPS-ARM is a useful tool for information to be used in further experimental investigations. The GPS-ARM is freely accessible for academic researchers at: http://arm.biocuckoo.org.
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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.