AIMC Topic: Phosphorylation

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DeepPhoPred: Accurate Deep Learning Model to Predict Microbial Phosphorylation.

Proteins Sep 6, 2024
Phosphorylation is a substantial posttranslational modification of proteins that refers to adding a phosphate group to the amino acid side chain after translation process in the ribosome. It is vital to coordinate cellular functions, such as regulati...
Computational Biology Protein Processing, Post-Translational Databases, Protein Software Deep Learning Phosphoproteins Serine Threonine Neural Networks, Computer Phosphorylation Bacterial Proteins
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Res-GCN: Identification of protein phosphorylation sites using graph convolutional network and residual network.

Computational biology and chemistry Aug 24, 2024
An essential post-translational modification, phosphorylation is intimately related with a wide range of biological activities. The advancement of effective computational methods for correctly recognizing phosphorylation sites is important for in-dep...
Humans Neural Networks, Computer Protein Processing, Post-Translational Phosphorylation SARS-CoV-2 Computational Biology
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PhosBERT: A self-supervised learning model for identifying phosphorylation sites in SARS-CoV-2-infected human cells.

Methods (San Diego, Calif.) Aug 22, 2024
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded RNA virus, which mainly causes respiratory and enteric diseases and is responsible for the outbreak of coronavirus disease 19 (COVID-19). Numerous studies have demonstr...
Humans Computational Biology Neural Networks, Computer SARS-CoV-2 Supervised Machine Learning Phosphorylation Spike Glycoprotein, Coronavirus Protein Processing, Post-Translational COVID-19
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PTransIPs: Identification of Phosphorylation Sites Enhanced by Protein PLM Embeddings.

IEEE journal of biomedical and health informatics Jun 6, 2024
Phosphorylation is pivotal in numerous fundamental cellular processes and plays a significant role in the onset and progression of various diseases. The accurate identification of these phosphorylation sites is crucial for unraveling the molecular me...
Sequence Analysis, Protein A549 Cells Amino Acid Sequence Humans Proteins Phosphorylation Deep Learning
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Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning.

Molecules (Basel, Switzerland) May 15, 2024
The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the ph...
Guanosine Triphosphate Protein Conformation Proto-Oncogene Proteins p21(ras) Humans Protein Binding Principal Component Analysis Phosphorylation Molecular Dynamics Simulation Deep Learning
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PhosAF: An integrated deep learning architecture for predicting protein phosphorylation sites with AlphaFold2 predicted structures.

Analytical biochemistry Mar 19, 2024
Phosphorylation is indispensable in comprehending biological processes, while biological experimental methods for identifying phosphorylation sites are tedious and arduous. With the rapid growth of biotechnology, deep learning methods have made signi...
Proteins Phosphorylation Neural Networks, Computer Deep Learning Humans
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Identifying Protein Phosphorylation Site-Disease Associations Based on Multi-Similarity Fusion and Negative Sample Selection by Convolutional Neural Network.

Interdisciplinary sciences, computational life sciences Mar 8, 2024
As one of the most important post-translational modifications (PTMs), protein phosphorylation plays a key role in a variety of biological processes. Many studies have shown that protein phosphorylation is associated with various human diseases. There...
Neural Networks, Computer Alzheimer Disease Protein Processing, Post-Translational Algorithms ROC Curve Humans Computational Biology Proteins Phosphorylation
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DeepNphos: A deep-learning architecture for prediction of N-phosphorylation sites.

Computers in biology and medicine Jan 28, 2024
MOTIVATION: Phosphorylation, a prevalent post-translational modification, plays a crucial role in regulating cellular activities. This process encompasses O-phosphorylation (e.g., phosphoserine) and N-phosphorylation (e.g., phospho-lysine (pK), phosp...
Histidine Arginine Lysine Protein Processing, Post-Translational Phosphorylation Deep Learning
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DL-SPhos: Prediction of serine phosphorylation sites using transformer language model.

Computers in biology and medicine Jan 3, 2024
Serine phosphorylation plays a pivotal role in the pathogenesis of various cellular processes and diseases. Roughly 81% of human diseases have links to phosphorylation, and an overwhelming 86.4% of protein phosphorylation takes place at serine residu...
Humans Serine Neural Networks, Computer Phosphorylation Animals Amino Acid Sequence Proteins Mammals
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Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification.

Molecular & cellular proteomics : MCP Dec 26, 2023
Shotgun phosphoproteomics enables high-throughput analysis of phosphopeptides in biological samples. One of the primary challenges associated with this technology is the relatively low rate of phosphopeptide identification during data analysis. This ...
Phosphorylation Phosphopeptides Liver Neoplasms Proteomics Humans Deep Learning
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