ArticlePloS one2011
Calpain cleavage prediction using multiple kernel learning.
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 49 papers.
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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.
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Who cites it
49 citing papers in PubMed, 88 citations in OpenAlex.
- Regulation of cell adhesion and migration by Kindlin-3 cleavage by calpain.The Journal of biological chemistry · 2012Trial
- DiCleave: a deep learning model for predicting human Dicer cleavage sites.BMC bioinformatics · 2024Article
- The protease calpain2a limits innate immunity by targeting TRAF6 in teleost fish.Communications biology · 2023Article
- Olfactory marker protein is unlikely to be cleaved by calpain 5.Molecular brain · 2022Article
- Calpain-mediated proteolysis as driver and modulator of polyglutamine toxicity.Frontiers in molecular neuroscience · 2022Review
- Inducible Depletion of Calpain-2 Mitigates Abdominal Aortic Aneurysm in Mice.Arteriosclerosis, thrombosis, and vascular biology · 2021Article
- ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites.BMC bioinformatics · 2021Article
- A novel cell-penetrating peptide targeting calpain-cleavage of PSD-95 induced by excitotoxicity improves neurological outcome after stroke.Theranostics · 2021Article
- Cytosolic calcium regulates cytoplasmic accumulation of TDP-43 through Calpain-A and Importin α3.eLife · 2020Article
- Calpain-2 participates in the process of calpain-1 inactivation.Bioscience reports · 2020Article
- Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.Briefings in bioinformatics · 2019Review
- Reduced SNAP25 Protein Fragmentation Contributes to SNARE Complex Dysregulation in Schizophrenia Postmortem Brain.Neuroscience · 2019Article
- Prevention of excitotoxicity-induced processing of BDNF receptor TrkB-FL leads to stroke neuroprotection.EMBO molecular medicine · 2019Article
- TET2 missense variants in human neoplasia. A proposal of structural and functional classification.Molecular genetics & genomic medicine · 2019Article
- Mitochondrial and calcium perturbations in rat CNS neurons induce calpain-cleavage of Parkin: Phosphatase inhibition stabilizes pSerBiochimica et biophysica acta. Molecular basis of disease · 2019Article
- Calcium-Activated Calpain Specifically Cleaves Glutamate Receptor IIA But Not IIB at theThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2019Article
- Ablation of the calpain-targeted site in cardiac myosin binding protein-C is cardioprotective during ischemia-reperfusion injury.Journal of molecular and cellular cardiology · 2019Article
- iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites.Briefings in bioinformatics · 2019Review
- Killing Two Angry Birds with One Stone: Autophagy Activation by Inhibiting Calpains in Neurodegenerative Diseases and Beyond.BioMed research international · 2019Review
- Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer.Frontiers in genetics · 2019Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Calpain, an intracellular Ca²⁺-dependent cysteine protease, is known to play a role in a wide range of metabolic pathways through limited proteolysis of its substrates. However, only a limited number of these substrates are currently known, with the exact mechanism of substrate recognition and cleavage by calpain still largely unknown. While previous research has successfully applied standard machine-learning algorithms to accurately predict substrate cleavage by other similar types of proteases, their approach does not extend well to calpain, possibly due to its particular mode of proteolytic action and limited amount of experimental data. Through the use of Multiple Kernel Learning, a recent extension to the classic Support Vector Machine framework, we were able to train complex models based on rich, heterogeneous feature sets, leading to significantly improved prediction quality (6% over highest AUC score produced by state-of-the-art methods). In addition to producing a stronger machine-learning model for the prediction of calpain cleavage, we were able to highlight the importance and role of each feature of substrate sequences in defining specificity: primary sequence, secondary structure and solvent accessibility. Most notably, we showed there existed significant specificity differences across calpain sub-types, despite previous assumption to the contrary. Prediction accuracy was further successfully validated using, as an unbiased test set, mutated sequences of calpastatin (endogenous inhibitor of calpain) modified to no longer block calpain's proteolytic action. An online implementation of our prediction tool is available at http://calpain.org.
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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.