AIMC Topic: Protein Binding

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Unveiling G-protein coupled receptor kinase-5 inhibitors for chronic degenerative diseases: Multilayered prioritization employing explainable machine learning-driven multi-class QSAR, ligand-based pharmacophore and free energy-inspired molecular simulation.

International journal of biological macromolecules Apr 30, 2024
GRK5 holds a pivotal role in cellular signaling pathways, with its overexpression in cardiomyocytes, neuronal cells, and tumor cells strongly associated with various chronic degenerative diseases, which highlights the urgent need for potential inhibi...
Chronic Disease Molecular Dynamics Simulation Ligands Molecular Docking Simulation Protein Binding Thermodynamics Pharmacophore G-Protein-Coupled Receptor Kinase 5 Quantitative Structure-Activity Relationship Protein Kinase Inhibitors Binding Sites Humans Machine Learning
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Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells.

Science (New York, N.Y.) Apr 26, 2024
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advan...
Protein Binding Proteomics Proteome Ligands Ubiquitin-Protein Ligases Small Molecule Libraries Humans Machine Learning Drug Discovery
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Co-Mutations and Possible Variation Tendency of the Spike RBD and Membrane Protein in SARS-CoV-2 by Machine Learning.

International journal of molecular sciences Apr 25, 2024
Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, SARS-CoV-2 variants capable of breakthrough infections have attracted global attention. These variants have significant mutations in the receptor-binding domain (RBD) of the spike p...
Spike Glycoprotein, Coronavirus Humans Protein Domains COVID-19 Machine Learning Mutation SARS-CoV-2 Amino Acid Sequence Protein Binding Coronavirus M Proteins
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Predicting FFAR4 agonists using structure-based machine learning approach based on molecular fingerprints.

Scientific reports Apr 24, 2024
Free Fatty Acid Receptor 4 (FFAR4), a G-protein-coupled receptor, is responsible for triggering intracellular signaling pathways that regulate various physiological processes. FFAR4 agonists are associated with enhancing insulin release and mitigatin...
Bayes Theorem Molecular Docking Simulation Binding Sites Molecular Dynamics Simulation Humans Ligands Protein Binding Machine Learning Receptors, G-Protein-Coupled
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Prospective de novo drug design with deep interactome learning.

Nature communications Apr 22, 2024
De novo drug design aims to generate molecules from scratch that possess specific chemical and pharmacological properties. We present a computational approach utilizing interactome-based deep learning for ligand- and structure-based generation of dru...
Ligands PPAR gamma Binding Sites Deep Learning Humans Protein Binding Drug Design
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Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning.

Molecules (Basel, Switzerland) Apr 19, 2024
Bromodomain 4 and 9 (BRD4 and BRD9) have been regarded as important targets of drug designs in regard to the treatment of multiple diseases. In our current study, molecular dynamics (MD) simulations, deep learning (DL) and binding free energy calcula...
Deep Learning Protein Binding Azepines Nuclear Proteins Bromodomain Containing Proteins Cell Cycle Proteins Humans Transcription Factors Molecular Docking Simulation Binding Sites Thermodynamics Molecular Dynamics Simulation Triazoles
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Encoding the space of protein-protein binding interfaces by artificial intelligence.

Computational biology and chemistry Apr 18, 2024
The physical interactions between proteins are largely determined by the structural properties at their binding interfaces. It was found that the binding interfaces in distinctive protein complexes are highly similar. The structural properties underl...
Artificial Intelligence Protein Binding Proteins Models, Molecular Protein Conformation Binding Sites
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ProtTrans and multi-window scanning convolutional neural networks for the prediction of protein-peptide interaction sites.

Journal of molecular graphics & modelling Apr 17, 2024
This study delves into the prediction of protein-peptide interactions using advanced machine learning techniques, comparing models such as sequence-based, standard CNNs, and traditional classifiers. Leveraging pre-trained language models and multi-vi...
Machine Learning Algorithms Peptides Humans Neural Networks, Computer Databases, Protein Binding Sites Protein Binding Computational Biology Proteins
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Genome-scale annotation of protein binding sites via language model and geometric deep learning.

eLife Apr 17, 2024
Revealing protein binding sites with other molecules, such as nucleic acids, peptides, or small ligands, sheds light on disease mechanism elucidation and novel drug design. With the explosive growth of proteins in sequence databases, how to accuratel...
Peptides Proteins Binding Sites Deep Learning Protein Binding
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PeSTo-Carbs: Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces.

Journal of chemical theory and computation Apr 11, 2024
The Protein Structure Transformer (PeSTo), a geometric transformer, has exhibited exceptional performance in predicting protein-protein binding interfaces and distinguishing interfaces with nucleic acids, lipids, small molecules, and ions. In this st...
Protein Binding Proteins Carbohydrates Binding Sites Deep Learning
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