AIMC Topic: Protein Processing, Post-Translational

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LSTMCNNsucc: A Bidirectional LSTM and CNN-Based Deep Learning Method for Predicting Lysine Succinylation Sites.

BioMed research international
Lysine succinylation is a typical protein post-translational modification and plays a crucial role of regulation in the cellular process. Identifying succinylation sites is fundamental to explore its functions. Although many computational methods wer...

PredNTS: Improved and Robust Prediction of Nitrotyrosine Sites by Integrating Multiple Sequence Features.

International journal of molecular sciences
Nitrotyrosine, which is generated by numerous reactive nitrogen species, is a type of protein post-translational modification. Identification of site-specific nitration modification on tyrosine is a prerequisite to understanding the molecular functio...

Computational identification of ubiquitination sites in Arabidopsis thaliana using convolutional neural networks.

Plant molecular biology
We developed two CNNs for predicting ubiquitination sites in Arabidopsis thaliana, demonstrated their competitive performance, analyzed amino acid physicochemical properties and the CNN structures, and predicted ubiquitination sites in Arabidopsis. A...

Prediction and analysis of redox-sensitive cysteines using machine learning and statistical methods.

Biological chemistry
Reactive oxygen species are produced by a number of stimuli and can lead both to irreversible intracellular damage and signaling through reversible post-translational modification. It is unclear which factors contribute to the sensitivity of cysteine...

RAM-PGK: Prediction of Lysine Phosphoglycerylation Based on Residue Adjacency Matrix.

Genes
BACKGROUND: Post-translational modification (PTM) is a biological process that is associated with the modification of proteome, which results in the alteration of normal cell biology and pathogenesis. There have been numerous PTM reports in recent ye...

PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids.

Genes
Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant...

Deep Learning in Proteomics.

Proteomics
Proteomics, the study of all the proteins in biological systems, is becoming a data-rich science. Protein sequences and structures are comprehensively catalogued in online databases. With recent advancements in tandem mass spectrometry (MS) technolog...

rPTMDetermine: A Fully Automated Methodology for Endogenous Tyrosine Nitration Validation, Site-Localization, and Beyond.

Analytical chemistry
We present herein rPTMDetermine, an adaptive and fully automated methodology for validation of the identification of rarely occurring post-translational modifications (PTMs), using a semisupervised approach with a linear discriminant analysis (LDA) a...

Accurate prediction of species-specific 2-hydroxyisobutyrylation sites based on machine learning frameworks.

Analytical biochemistry
Lysine 2-hydroxyisobutyrylation (K) is a newly discovered post-translational modification (PTM) across eukaryotes and prokaryotes in recent years, which plays a significant role in diverse cellular functions. Accurate prediction of K sites is a first...