AIMC Topic: Protein Binding

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AI-designed PNA-peptide chimera overcomes suboptimal binding for dual inhibition of viral RdRp.

European journal of medicinal chemistry Nov 16, 2025
The chimera combining the peptide nucleic acids (PNAs) and peptides represent a promising bifunctional strategy by concurrently binding with protein catalytic pocket and its associated RNA template, effectively disrupting protein's function. Conventi...
SARS-CoV-2 Peptides Drug Design Humans Artificial Intelligence Antiviral Agents Peptide Nucleic Acids Protein Binding Thermodynamics RNA-Dependent RNA Polymerase
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RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking.

Journal of chemical information and modeling Nov 13, 2025
Accurate identification of druggable pockets and their features is essential for structure-based drug design and effective downstream docking. Here, we present RAPID-Net, a deep learning-based algorithm designed for accurate prediction of binding poc...
SARS-CoV-2 Ligands Deep Learning Humans Molecular Docking Simulation Protein Binding Algorithms Proteins Drug Design Binding Sites
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How Feasible Is Docking of PROTACs to POI-E3L Complexes? Testing Physics-Based and ML-Based Docking Tools.

Journal of chemical information and modeling Nov 12, 2025
Targeted protein degradation (TPD) is an innovative drug discovery approach that leverages small molecules to induce proximity between a protein of interest (POI) and an E3 ubiquitin ligase (E3L) for selective degradation. Among TPD modalities, prote...
Machine Learning Molecular Docking Simulation Drug Discovery Ubiquitin-Protein Ligases Proteolysis Proteolysis Targeting Chimera Protein Binding Feasibility Studies
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Asymmetric Dynamics Between the Protomers of the σ2 Receptor Homodimer.

Journal of chemical information and modeling Nov 6, 2025
The sigma-2 receptor (σR/TMEM97) is a clinically relevant membrane protein involved in cholesterol regulation and overexpressed in cancer and neurodegenerative diseases. Despite its therapeutic potential, the dynamic mechanisms underlying σR function...
Protein Multimerization Receptors, sigma Humans Cholesterol Molecular Dynamics Simulation Protein Binding
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Delineating SARS-CoV-2 spike protein and antibodies interaction interfaces via siamese neural networks: A geometric and image-based analysis.

PloS one Nov 4, 2025
The analysis of molecular interactions between antigens and antibodies is crucial for understanding the immunological mechanisms underlying the immune response and for developing effective therapies against various diseases. In this context, the abil...
Spike Glycoprotein, Coronavirus Deep Learning Protein Binding Antibodies, Viral COVID-19 Humans Neural Networks, Computer SARS-CoV-2
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Characterization of binding kinetics and intracellular signaling of new psychoactive substances targeting cannabinoid receptor using transition-based reweighting method.

eLife Nov 3, 2025
New psychoactive substances (NPS) targeting human cannabinoid receptor 1 pose a significant threat to society as recreational abusive drugs that have pronounced physiological side effects. These greater adverse effects compared to classical cannabino...
Humans Cannabinoids Receptors, Cannabinoid Receptor, Cannabinoid, CB1 Protein Binding Kinetics Molecular Dynamics Simulation Signal Transduction Psychotropic Drugs
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Learning Binding Affinities via Fine-Tuning of Protein and Ligand Language Models.

Journal of chemical information and modeling Oct 31, 2025
Accurate in silico prediction of protein-ligand binding affinity is essential for efficient hit identification in large molecular libraries. Commonly used structure-based methods such as docking often fail to rank compounds effectively, and free ener...
Deep Learning Machine Learning Molecular Docking Simulation Ligands Proteins Drug Discovery Protein Binding
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A novel prediction method for protein-DNA binding sites based on protein language model fusion features with SE-connection pyramidal network and ensemble learning.

BMC genomics Oct 30, 2025
Protein-DNA interactions are crucial in life processes such as gene expression and regulation. Therefore, the accurate prediction of DNA-binding sites on proteins is highly important for the advancement of scientific understanding in the field of bio...
Binding Sites Ensemble Learning Machine Learning Computational Biology Algorithms DNA Protein Binding DNA-Binding Proteins
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Kideraspa: designing variants of staphylococcal protein a based on a diffusion model with kidera factors.

Journal of computer-aided molecular design Oct 24, 2025
The interaction between staphylococcal protein A (SpA) and human immunoglobulin G (IgG) is pivotal in treating diseases such as cancer, inflammation, infections, and autoimmune disorders. However, acquiring natural SpA variants is labor-intensive, tr...
Protein Engineering Staphylococcal Protein A Mutation Humans Binding Sites Immunoglobulin G Protein Binding Deep Learning Models, Molecular
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A generalizable deep learning framework for structure-based protein-ligand affinity ranking.

Proceedings of the National Academy of Sciences of the United States of America Oct 16, 2025
Rapid and accurate estimation of protein-ligand binding affinities is crucial for early-stage drug discovery, yet hindered by a trade-off between the accuracy of gold-standard physics-based methods and the speed of simpler empirical scoring functions...
Drug Discovery Proteins Deep Learning Ligands Protein Binding
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