AIMC Topic: Signal Transduction

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Deep-Learning-Enhanced Diffusion Imaging Assay for Resolving Local-Density Effects on Membrane Receptors.

Analytical chemistry Jan 30, 2023
G-protein-coupled receptor (GPCR) density at the cell surface is thought to regulate receptor function. Spatially resolved measurements of local-density effects on GPCRs are needed but technically limited by density heterogeneity and mobility of memb...
Ligands Cell Membrane Drug Inverse Agonism Deep Learning Signal Transduction Receptors, G-Protein-Coupled
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Decoding CAR T cell phenotype using combinatorial signaling motif libraries and machine learning.

Science (New York, N.Y.) Dec 8, 2022
Chimeric antigen receptor (CAR) costimulatory domains derived from native immune receptors steer the phenotypic output of therapeutic T cells. We constructed a library of CARs containing ~2300 synthetic costimulatory domains, built from combinations ...
Signal Transduction Protein Domains T-Lymphocytes, Cytotoxic Humans Machine Learning Phenotype Receptors, Chimeric Antigen Peptide Library
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Multi-source transfer learning with Graph Neural Network for excellent modelling the bioactivities of ligands targeting orphan G protein-coupled receptors.

Mathematical biosciences and engineering : MBE Nov 25, 2022
G protein-coupled receptors (GPCRs) have been the targets for more than 40% of the currently approved drugs. Although neural networks can effectively improve the accuracy of prediction with the biological activity, the result is undesirable in the li...
Signal Transduction Receptors, G-Protein-Coupled Ligands Neural Networks, Computer Machine Learning
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Multimodal multi-task deep neural network framework for kinase-target prediction.

Molecular diversity Nov 11, 2022
Kinase plays a significant role in various disease signaling pathways. Due to the highly conserved sequence of kinase family members, understanding the selectivity profile of kinase inhibitors remains a priority for drug discovery. Previous methods f...
Neural Networks, Computer Drug Discovery Signal Transduction Proteins
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Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins.

eLife Oct 13, 2022
A fundamental question in protein science is where allosteric hotspots - residues critical for allosteric signaling - are located, and what properties differentiate them. We carried out deep mutational scanning (DMS) of four homologous bacterial allo...
Mutation Molecular Dynamics Simulation Allosteric Regulation Machine Learning Signal Transduction Proteins
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Deep learning for de-convolution of Smad2 versus Smad3 binding sites.

BMC genomics Jul 20, 2022
BACKGROUND: The transforming growth factor beta-1 (TGF β-1) cytokine exerts both pro-tumor and anti-tumor effects in carcinogenesis. An increasing body of literature suggests that TGF β-1 signaling outcome is partially dependent on the regulatory tar...
Smad2 Protein Smad3 Protein Binding Sites Deep Learning Signal Transduction Cell Line Transforming Growth Factor beta
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Quantifying information of intracellular signaling: progress with machine learning.

Reports on progress in physics. Physical Society (Great Britain) Jul 12, 2022
Cells convey information about their extracellular environment to their core functional machineries. Studying the capacity of intracellular signaling pathways to transmit information addresses fundamental questions about living systems. Here, we revi...
Machine Learning Signal Transduction
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The immuneoreaction and antioxidant status of Chinese mitten crab (Eriocheir sinensis) involve protein metabolism and the response of mTOR signaling pathway to dietary methionine levels.

Fish & shellfish immunology Jul 8, 2022
To study the effects of dietary methionine on growth performance, immunity, antioxidant capacity, protein metabolism, inflammatory response and apoptosis factors in Chinese mitten crabs (Eriocheir sinensis). Five diets with different methionine level...
Methionine Brachyura Animals China Sirolimus Immunity, Innate TOR Serine-Threonine Kinases Diet Antioxidants Dietary Supplements Animal Feed Signal Transduction Mammals
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Combining explainable machine learning, demographic and multi-omic data to inform precision medicine strategies for inflammatory bowel disease.

PloS one Feb 23, 2022
Inflammatory bowel diseases (IBDs), including ulcerative colitis and Crohn's disease, affect several million individuals worldwide. These diseases are heterogeneous at the clinical, immunological and genetic levels and result from complex host and en...
Prednisolone Mesalamine Pyrazoles Phenylurea Compounds Naphthalenes Crohn Disease Drug Evaluation, Preclinical Transcriptome Adolescent Humans Genomics Adult Machine Learning Signal Transduction Male Female Tumor Necrosis Factor-alpha Colitis, Ulcerative Middle Aged Anti-Inflammatory Agents, Non-Steroidal Aged Precision Medicine Young Adult
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Machine Learning Identifies Pan-Cancer Landscape of Nrf2 Oxidative Stress Response Pathway-Related Genes.

Oxidative medicine and cellular longevity Feb 17, 2022
BACKGROUND: Oxidative stress produced a large amount of reactive oxygen species (ROS), which played a pivotal role in balanced ability and determining cell fate. The activated Nrf2 signaling pathway that responds to the excessive ROS regulated the ex...
Humans Mutation Rate Machine Learning Biomarkers, Tumor NF-E2-Related Factor 2 Phenotype Prognosis Gene Expression Regulation, Neoplastic Neoplasms Case-Control Studies Survival Rate Signal Transduction Transcriptome Oxidative Stress Tumor Microenvironment Reactive Oxygen Species
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