AIMC Topic: Protein Binding

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T cell receptor specificity landscape revealed through de novo peptide design.

Proceedings of the National Academy of Sciences of the United States of America Oct 16, 2025
T cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. Effective bindings between T cell receptors (TCRs) and pathogen derived peptides presented on major histocompatibility complexes (MHCs) mediate imm...
Humans Machine Learning T-Lymphocytes Protein Binding Histocompatibility Antigens Class I Major Histocompatibility Complex Peptides Receptors, Antigen, T-Cell
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TEMPL: A Template-Based Protein-Ligand Pose Prediction Baseline.

Journal of chemical information and modeling Oct 14, 2025
Pose prediction of ligands to proteins remains a central challenge of structure-based drug design. Although data leakage and generalizability concerns remain, data-driven methods for pose prediction (i.e., based on deep learning and diffusion) now ro...
Ligands Protein Conformation Drug Design Deep Learning Algorithms Protein Binding Proteins SARS-CoV-2 Antiviral Agents Humans Molecular Docking Simulation
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Investigating whether deep learning models for co-folding learn the physics of protein-ligand interactions.

Nature communications Oct 6, 2025
Co-folding models represent a major innovation in deep-learning-based protein-ligand structure prediction. The recent publications of RoseTTAFold All-Atom, AlphaFold3, and others have shown high-quality results on predicting the structures of protein...
Protein Folding Protein Binding Proteins Ligands Protein Conformation Models, Molecular Deep Learning
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AI-driven protein pocket detection through integrating deep Q-networks for structural analysis.

Journal of computer-aided molecular design Oct 6, 2025
Protein pockets, or small cavities on the protein surface, are critical sites for enzymatic catalysis, molecular recognition, and drug binding. Accurately identifying these pockets is crucial for understanding protein function and designing therapeut...
Algorithms Molecular Docking Simulation Deep Learning Humans Databases, Protein Molecular Dynamics Simulation Protein Conformation Protein Binding Proteins Binding Sites
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ML-PLA: Enhancing Protein-Ligand Binding Affinity Prediction with Microenvironment and Long-Range Interaction-Aware Graph Neural Networks.

Journal of chemical information and modeling Oct 3, 2025
Accurately predicting protein-ligand binding affinity (PLA) is essential in drug discovery for identifying lead compounds. The sequence and structural contexts of an amino acid residue (i.e., microenvironment) describe the surrounding chemical proper...
Graph Neural Networks Proteins Ligands Drug Discovery Protein Binding Neural Networks, Computer
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GENEOnet: a breakthrough in protein binding pocket detection using group equivariant non-expansive operators.

Scientific reports Oct 3, 2025
Structure-based virtual screening approaches like molecular docking rely on accurately identifying and precisely calculating binding pockets to efficiently search for potential ligands. In this paper, we introduce GENEOnet, a machine learning model d...
Humans Machine Learning Ligands Binding Sites Protein Binding Molecular Docking Simulation Software Proteins Algorithms
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Robust Prediction of Protein-Ligand Binding Potency with Multi-modal Customized Gate Control.

Journal of chemical information and modeling Sep 25, 2025
The main protease (Mpro) is a critical target in the design of antiviral drugs against coronaviruses, while accurately predicting the binding affinity between small molecules and this target remains a key challenge. In the recent Polaris challenge of...
Deep Learning Antiviral Agents Humans Ligands Protein Binding SARS-CoV-2 COVID-19 Drug Treatment
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Structure based drug design and machine learning approaches for identifying natural inhibitors against the human αβIII tubulin isotype.

Scientific reports Sep 24, 2025
Microtubules (MTs) play a crucial role in mitosis and are composed of α-/β-tubulin heterodimeric subunits. In eukaryotes, eight α-tubulin and ten β-tubulin isotypes have been reported, each displaying tissue-specific expression patterns. Among them, ...
Tubulin Binding Sites Tubulin Modulators Biological Products Molecular Dynamics Simulation Drug Design Protein Binding Humans Machine Learning Molecular Docking Simulation
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PPAP: A Protein-protein Affinity Predictor Incorporating Interfacial Contact-Aware Attention.

Journal of chemical information and modeling Sep 19, 2025
Protein-protein interactions (PPIs) play fundamental roles in biological processes and therapeutic development. Accurately predicting PPI binding affinity is critical for understanding interaction mechanisms and guiding protein engineering. Recent ad...
Deep Learning Models, Molecular Protein Binding Proteins Protein Interaction Mapping
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Revisiting Protein-Protein Docking: A Systematic Evaluation Framework.

Journal of chemical information and modeling Sep 18, 2025
Protein-protein interactions play pivotal roles in a wide range of biological processes. Determining the atomic-level structures of protein-protein complexes is indispensable for elucidating macromolecular interaction mechanisms and advancing structu...
Proteins Protein Conformation Molecular Docking Simulation Protein Binding
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