AIMC Topic: Protein Processing, Post-Translational

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MDD-SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs.

Bioinformatics (Oxford, England)
UNLABELLED: S-sulfenylation (S-sulphenylation, or sulfenic acid), the covalent attachment of S-hydroxyl (-SOH) to cysteine thiol, plays a significant role in redox regulation of protein functions. Although sulfenic acid is transient and labile, most ...

jEcho: an Evolved weight vector to CHaracterize the protein's posttranslational modification mOtifs.

Interdisciplinary sciences, computational life sciences
Protein's posttranslational modification (PTM) represents a major dynamic regulation of protein functions after the translation of polypeptide chains from mRNA molecule. Compared with the costly and labor-intensive wet laboratory characterization of ...

Accurate in silico identification of protein succinylation sites using an iterative semi-supervised learning technique.

Journal of theoretical biology
As a widespread type of protein post-translational modifications (PTMs), succinylation plays an important role in regulating protein conformation, function and physicochemical properties. Compared with the labor-intensive and time-consuming experimen...

Types and effects of protein variations.

Human genetics
Variations in proteins have very large number of diverse effects affecting sequence, structure, stability, interactions, activity, abundance and other properties. Although protein-coding exons cover just over 1 % of the human genome they harbor an di...

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.

Bioinformatics (Oxford, England)
MOTIVATION: Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes (BPs) such as cellular communication, ligand recognition and subcellular reco...

An effective statistical moment-based feature extraction technique to identify the phosphoglycerylation sites from protein sequences.

Journal of molecular graphics & modelling
A kind of covalent modification known as post-translational modification (PTM) happens following the biosynthesis process, which is important in cell biology research. A reversible PTM called Lysine phosphoglycerylation alters glycolytic enzyme activ...

Decoding Glycosylation in Neurodegenerative Diseases: Mechanistic Insights and Therapeutic Opportunities.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Glycosylation is a highly dynamic and complex post-translational modification that plays a pivotal role in regulating protein folding, trafficking, stability, and function. Accumulating evidence indicates that aberrant glycosylation is intimately inv...

DeepMS: super-fast peptide identification using end-to-end deep learning method.

Journal of molecular biology
Mass spectrometry (MS) has emerged as a powerful omics analysis technique, particularly in proteomics, where the initial step involves identifying MS spectra as peptide sequences. However, this process often requires substantial computational resourc...

Why Protein Modifications Matter for Digestibility: The Case of Ara h 1 Peanut Allergen and Trypsin Cleavage.

Journal of agricultural and food chemistry
Trypsin is the principal intestinal endopeptidase and proteomics digestion tool, yet the impact of protein modifications (PMs) on digestibility and allergenicity remains underexplored. We employed a proteomic approach to assess trypsin cleavage effic...

A deep learning model for prediction of lysine crotonylation sites by fusing multi-features based on multi-head self-attention mechanism.

Scientific reports
Lysine crotonylation (Kcr) is an important post-translational modification, which is present in both histone and non-histone proteins, and plays a key role in a variety of biological processes such as metabolism and cell differentiation. Therefore, r...