AIMC Topic: Phosphorylation

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DeepMPSF: A Deep Learning Network for Predicting General Protein Phosphorylation Sites Based on Multiple Protein Sequence Features.

Journal of chemical information and modeling Nov 6, 2023
Phosphorylation, as one of the most important post-translational modifications, plays a key role in various cellular physiological processes and disease occurrences. In recent years, computer technology has been gradually applied to the prediction of...
Mice Rats Animals Deep Learning Phosphorylation Amino Acid Sequence Protein Processing, Post-Translational Proteins Humans
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A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction.

Genomics, proteomics & bioinformatics Oct 19, 2023
Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and, as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that...
Humans Machine Learning Proteins Databases, Protein Phosphorylation Algorithms Computational Biology Animals Protein Processing, Post-Translational
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LMPhosSite: A Deep Learning-Based Approach for General Protein Phosphorylation Site Prediction Using Embeddings from the Local Window Sequence and Pretrained Protein Language Model.

Journal of proteome research Jul 17, 2023
Phosphorylation is one of the most important post-translational modifications and plays a pivotal role in various cellular processes. Although there exist several computational tools to predict phosphorylation sites, existing tools have not yet harne...
Protein Processing, Post-Translational Proteins Deep Learning Phosphorylation Amino Acid Sequence
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Large-Scale Modeling of Sparse Protein Kinase Activity Data.

Journal of chemical information and modeling Jun 9, 2023
Protein kinases are a protein family that plays an important role in several complex diseases such as cancer and cardiovascular and immunological diseases. Protein kinases have conserved ATP binding sites, which when targeted can lead to similar acti...
Protein Kinases Proteins Phosphorylation Machine Learning Protein Processing, Post-Translational
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Sequence-based machine learning method for predicting the effects of phosphorylation on protein-protein interactions.

International journal of biological macromolecules Jun 6, 2023
Protein phosphorylation, catalyzed by kinases, is an important biochemical process, which plays an essential role in multiple cell signaling pathways. Meanwhile, protein-protein interactions (PPI) constitute the signaling pathways. Abnormal phosphory...
Phosphorylation Machine Learning Computational Biology Signal Transduction Proteins Artificial Intelligence
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Multiplex Identification of Post-Translational Modifications at Point-of-Care by Deep Learning-Assisted Hydrogel Sensors.

Angewandte Chemie (International ed. in English) Mar 9, 2023
Multiplex detection of protein post-translational modifications (PTMs), especially at point-of-care, is of great significance in cancer diagnosis. Herein, we report a machine learning-assisted photonic crystal hydrogel (PCH) sensor for multiplex dete...
Animals Point-of-Care Systems Mammals Hydrogels Proteins Deep Learning Phosphorylation Protein Processing, Post-Translational
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Leveraging Protein Dynamics to Identify Functional Phosphorylation Sites using Deep Learning Models.

Journal of chemical information and modeling Jul 11, 2022
Accurate prediction of post-translational modifications (PTMs) is of great significance in understanding cellular processes, by modulating protein structure and dynamics. Nowadays, with the rapid growth of protein data at different "omics" levels, ma...
Phosphorylation Acetylation Protein Processing, Post-Translational Proteins Deep Learning
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Screening membraneless organelle participants with machine-learning models that integrate multimodal features.

Proceedings of the National Academy of Sciences of the United States of America Jun 10, 2022
Protein self-assembly is one of the formation mechanisms of biomolecular condensates. However, most phase-separating systems (PS) demand multiple partners in biological conditions. In this study, we divided PS proteins into two groups according to th...
Machine Learning Proteome Humans Biomolecular Condensates Organelles Proteins Internet Use Phosphorylation
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Kinases on Double Duty: A Review of UniProtKB Annotated Bifunctionality within the Kinome.

Biomolecules May 11, 2022
Phosphorylation facilitates the regulation of all fundamental biological processes, which has triggered extensive research of protein kinases and their roles in human health and disease. In addition to their phosphotransferase activity, certain kinas...
Knowledge Bases Humans Phosphorylation Protein Kinases
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TransPhos: A Deep-Learning Model for General Phosphorylation Site Prediction Based on Transformer-Encoder Architecture.

International journal of molecular sciences Apr 12, 2022
Protein phosphorylation is one of the most critical post-translational modifications of proteins in eukaryotes, which is essential for a variety of biological processes. Plenty of attempts have been made to improve the performance of computational pr...
Phosphorylation Protein Processing, Post-Translational Proteins Neural Networks, Computer Deep Learning
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