AIMC Topic: Phosphorylation
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GPS-PBS: A Deep Learning Framework to Predict Phosphorylation Sites that Specifically Interact with Phosphoprotein-Binding Domains.
Cells
May 20, 2020
Protein phosphorylation is essential for regulating cellular activities by modifying substrates at specific residues, which frequently interact with proteins containing phosphoprotein-binding domains (PPBDs) to propagate the phosphorylation signaling...
Artificial Intelligence Steering Molecular Therapy in the Absence of Information on Target Structure and Regulation.
Journal of chemical information and modeling
Dec 4, 2019
Protein associations are at the core of biological activity, and the drug-based disruption of dysfunctional associations poses a major challenge to targeted therapy. The problem becomes daunting when the structure and regulated modulation of the comp...
Automating Complex, Multistep Processes on a Single Robotic Platform to Generate Reproducible Phosphoproteomic Data.
SLAS discovery : advancing life sciences R & D
Sep 26, 2019
Mass spectrometry-based phosphoproteomics holds promise for advancing drug treatment and disease diagnosis; however, its clinical translation has thus far been limited. This is in part due to an unstandardized and segmented sample preparation process...
Boosting phosphorylation site prediction with sequence feature-based machine learning.
Proteins
Aug 22, 2019
Protein phosphorylation is one of the essential posttranslation modifications playing a vital role in the regulation of many fundamental cellular processes. We propose a LightGBM-based computational approach that uses evolutionary, geometric, sequenc...
Computational Biology
Protein Processing, Post-Translational
Proteins
Databases, Protein
Algorithms
Reproducibility of Results
Animals
Tyrosine
Binding Sites
Serine
Sequence Analysis, Protein
Phosphorylation
Models, Molecular
Protein Conformation
Species Specificity
Humans
Machine Learning
Threonine
Assessment of Functional Phosphatidylinositol 3-Kinase Pathway Activity in Cancer Tissue Using Forkhead Box-O Target Gene Expression in a Knowledge-Based Computational Model.
The American journal of pathology
Jul 6, 2018
The phosphatidylinositol 3-kinase (PI3K) pathway is commonly activated in cancer. Tumors are potentially sensitive to PI3K pathway inhibitors, but reliable diagnostic tests that assess functional PI3K activity are lacking. Because PI3K pathway activi...
Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates.
Molecular & cellular proteomics : MCP
Mar 6, 2017
Mass spectrometry allows quantification of tens of thousands of phosphorylation sites from minute amounts of cellular material. Despite this wealth of information, our understanding of phosphorylation-based signaling is limited, in part because it is...
Modulatory role of garlicin in migration and invasion of intrahepatic cholangiocarcinoma via PI3K/AKT pathway.
International journal of clinical and experimental pathology
Nov 1, 2015
Increasing evidences have indicated the role of garlicin in inhibiting the progression of various tumors including glioma, pulmonary carcinoma and pancreatic carcinoma, via mediating cell apoptosis or cell cycle. The regulatory effect and related mol...
Cholangiocarcinoma
Antineoplastic Agents, Phytogenic
Phosphatidylinositol 3-Kinase
Signal Transduction
Bile Duct Neoplasms
Phosphoinositide-3 Kinase Inhibitors
Humans
Cell Movement
Phosphorylation
Disulfides
Neoplasm Invasiveness
Cell Line, Tumor
Proto-Oncogene Proteins c-akt
Dose-Response Relationship, Drug
Allyl Compounds
Cell Proliferation
Protein Kinase Inhibitors
Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation.
BioMed research international
Oct 27, 2015
Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much at...
jEcho: an Evolved weight vector to CHaracterize the protein's posttranslational modification mOtifs.
Interdisciplinary sciences, computational life sciences
Aug 6, 2015
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 ...
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.
Nature methods
May 4, 2015
Protein phosphorylation is important in cellular pathways and altered in disease. We developed MIMP (http://mimp.baderlab.org/), a machine learning method to predict the impact of missense single-nucleotide variants (SNVs) on kinase-substrate interac...
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