AIMC Topic: Phosphorylation
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A Transfer-Learning-Based Deep Convolutional Neural Network for Predicting Leukemia-Related Phosphorylation Sites from Protein Primary Sequences.
International journal of molecular sciences
Feb 3, 2022
As one of the most important post-translational modifications (PTMs), phosphorylation refers to the binding of a phosphate group with amino acid residues like Ser (S), Thr (T) and Tyr (Y) thus resulting in diverse functions at the molecular level. Ab...
A novel graph convolutional neural network for predicting interaction sites on protein kinase inhibitors in phosphorylation.
Scientific reports
Jan 7, 2022
Protein kinase-inhibitor interactions are key to the phosphorylation of proteins involved in cell proliferation, differentiation, and apoptosis, which shows the importance of binding mechanism research and kinase inhibitor design. In this study, a no...
A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana.
BMC plant biology
Dec 14, 2021
BACKGROUND: Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to ...
Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification.
Molecular & cellular proteomics : MCP
Nov 1, 2021
Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human canc...
Non-invasive diagnostic tool for Parkinson's disease by sebum RNA profile with machine learning.
Scientific reports
Sep 20, 2021
Parkinson's disease (PD) is a progressive neurodegenerative disease presenting with motor and non-motor symptoms, including skin disorders (seborrheic dermatitis, bullous pemphigoid, and rosacea), skin pathological changes (decreased nerve endings an...
PARROT is a flexible recurrent neural network framework for analysis of large protein datasets.
eLife
Sep 17, 2021
The rise of high-throughput experiments has transformed how scientists approach biological questions. The ubiquity of large-scale assays that can test thousands of samples in a day has necessitated the development of new computational approaches to i...
A deep learning based approach for prediction of Chlamydomonas reinhardtii phosphorylation sites.
Scientific reports
Jun 15, 2021
Protein phosphorylation, which is one of the most important post-translational modifications (PTMs), is involved in regulating myriad cellular processes. Herein, we present a novel deep learning based approach for organism-specific protein phosphoryl...
Predicting phosphorylation sites using machine learning by integrating the sequence, structure, and functional information of proteins.
Journal of translational medicine
May 24, 2021
BACKGROUND: Post-translational modification (PTM) is a biological process that alters proteins and is therefore involved in the regulation of various cellular activities and pathogenesis. Protein phosphorylation is an essential process and one of the...
Application of deep learning to understand resilience to Alzheimer's disease pathology.
Brain pathology (Zurich, Switzerland)
May 19, 2021
People who have Alzheimer's disease neuropathologic change (ADNC) typically associated with dementia but not the associated cognitive decline can be considered to be "resilient" to the effects of ADNC. We have previously reported lower neocortical le...
iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition.
IEEE/ACM transactions on computational biology and bioinformatics
Apr 6, 2021
Protein phosphorylation is one of the key mechanism in prokaryotes and eukaryotes and is responsible for various biological functions such as protein degradation, intracellular localization, the multitude of cellular processes, molecular association,...
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