ArticleBMC bioinformatics2006
NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Palmitoyltransferase ZDHHC3 is essential for the oncogenic activity of PML/RARα in acute promyelocytic leukemia.Acta pharmacologica Sinica · 2025Article
- Topology-Driven Discovery of Transmembrane ProteinbioRxiv : the preprint server for biology · 2024Article
- Unveiling the defensive role of Snakin-3, a member of the subfamily III of Snakin/GASA peptides in potatoes.Plant cell reports · 2024Article
- Palmitoylation of solute carriers.Biochemical pharmacology · 2023Review
- S-Palmitoylation of Synaptic Proteins in Neuronal Plasticity in Normal and Pathological Brains.Cells · 2023Review
- Article
- Protein Lipidation Types: Current Strategies for Enrichment and Characterization.International journal of molecular sciences · 2022Review
- Article
- RFCM-PALM: In-Silico Prediction of S-Palmitoylation Sites in the Synaptic Proteins for Male/Female Mouse Data.International journal of molecular sciences · 2021Article
- Identification of Proteins of Tobacco Mosaic Virus by Using a Method of Feature Extraction.Frontiers in genetics · 2020Article
- Fatty Acid Synthase Promotes the Palmitoylation of Chikungunya Virus nsP1.Journal of virology · 2019Article
- An Information Entropy-Based Approach for Computationally Identifying Histone Lysine Butyrylation.Frontiers in genetics · 2019Article
- The unusual flagellar-targeting mechanism and functions of the trypanosome ortholog of the ciliary GTPase Arl13b.Journal of cell science · 2018Article
- Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies.Chemical reviews · 2018Article
- Article
- Protein Lipidation As a Regulator of Apoptotic Calcium Release: Relevance to Cancer.Frontiers in oncology · 2017Review
- MDD-Palm: Identification of protein S-palmitoylation sites with substrate motifs based on maximal dependence decomposition.PloS one · 2017Article
- Dynamic Regulation of N-Methyl-d-aspartate (NMDA) and α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors by Posttranslational Modifications.The Journal of biological chemistry · 2015Review
- Regulating Set-β's Subcellular Localization Toggles Its Function between Inhibiting and Promoting Axon Growth and Regeneration.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2014Article
- PalmPred: an SVM based palmitoylation prediction method using sequence profile information.PloS one · 2014Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProtein palmitoylation, an essential and reversible post-translational modification (PTM), has been implicated in cellular dynamics and plasticity. Although numerous experimental studies have been performed to explore the molecular mechanisms underlying palmitoylation processes, the intrinsic feature of substrate specificity has remained elusive. Thus, computational approaches for palmitoylation prediction are much desirable for further experimental design.
resultsIn this work, we present NBA-Palm, a novel computational method based on Naïve Bayes algorithm for prediction of palmitoylation site. The training data is curated from scientific literature (PubMed) and includes 245 palmitoylated sites from 105 distinct proteins after redundancy elimination. The proper window length for a potential palmitoylated peptide is optimized as six. To evaluate the prediction performance of NBA-Palm, 3-fold cross-validation, 8-fold cross-validation and Jack-Knife validation have been carried out. Prediction accuracies reach 85.79% for 3-fold cross-validation, 86.72% for 8-fold cross-validation and 86.74% for Jack-Knife validation. Two more algorithms, RBF network and support vector machine (SVM), also have been employed and compared with NBA-Palm.
conclusionTaken together, our analyses demonstrate that NBA-Palm is a useful computational program that provides insights for further experimentation. The accuracy of NBA-Palm is comparable with our previously described tool CSS-Palm. The NBA-Palm is freely accessible from: http://www.bioinfo.tsinghua.edu.cn/NBA-Palm.
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