AIMC Topic: Binding Sites

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HPDAF: A practical tool for predicting drug-target binding affinity using multimodal features.

European journal of medicinal chemistry Sep 8, 2025
Accurate prediction of drug-target binding affinity is crucial for efficient drug discovery and design, enabling researchers to better understand molecular interactions and accelerate the identification of promising drug candidates. Despite recent ad...
Humans Drug Design Drug Discovery Molecular Structure Deep Learning Pharmaceutical Preparations Protein Binding Binding Sites Proteins
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Advances and Challenges in Machine Learning for RNA-Small Molecule Interaction Modeling: Review.

Journal of chemical theory and computation Sep 8, 2025
RNA plays a pivotal role in biological processes such as gene expression regulation and protein synthesis. Targeting RNA with small molecules offers a novel therapeutic strategy for various diseases by directly modulating these processes. However, th...
Binding Sites Small Molecule Libraries Humans Machine Learning RNA
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Multiview Deep Learning Framework for Precise Prediction of Transcription Factor Binding Sites.

Journal of chemical information and modeling Sep 7, 2025
Transcription factors (TFs) are essential proteins that regulate gene expression by specifically binding to transcription factor binding sites (TFBSs) within DNA sequences. Their ability to precisely control the transcription process is crucial for u...
DNA Binding Sites Protein Binding Computational Biology Deep Learning Transcription Factors
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A Machine Learning Model for the Proteome-Wide Prediction of Lipid-Interacting Proteins.

Journal of chemical information and modeling Sep 4, 2025
Lipids are essential metabolites that play critical roles in multiple cellular pathways. Like many primary metabolites, mutations that disrupt lipid synthesis can be lethal. Proteins involved in lipid synthesis, trafficking, and modification, are tar...
Machine Learning Algorithms Protein Binding Humans Proteins Models, Molecular Hydrophobic and Hydrophilic Interactions Computational Biology Proteome Lipids Binding Sites
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GATRsite: RNA-Ligand Binding Site Prediction Using Graph Attention Networks and Pretrained RNA Language Models.

Journal of chemical information and modeling Aug 14, 2025
Identifying functional sites of RNA, particularly those where small molecules bind, is crucial for understanding related biological processes and advancing drug design. Small molecule therapies, compared to traditional protein-targeted therapies, hav...
Computational Biology Ligands Models, Molecular Deep Learning RNA Binding Sites
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Computer-Aided Techniques in the Engineering of Enzyme Binding Pockets: New Perspectives and Frontiers.

Journal of agricultural and food chemistry Aug 11, 2025
Enzymes, recognized for their remarkable catalytic efficiency, play a crucial role in a myriad of biochemical reactions. However, the catalytic performance of natural enzymes frequently does not meet the demands of specific applications. To address t...
Protein Engineering Enzymes Protein Conformation Binding Sites Biocatalysis
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CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches.

Journal of computer-aided molecular design Jul 13, 2025
Identifying orthosteric binding sites and predicting small molecule affinities remains a key challenge in virtual screening. While blind docking explores the entire protein surface, its precision is hindered by the vast search space. Cavity detection...
Proteins Ligands Protein Conformation Binding Sites Algorithms Molecular Docking Simulation Machine Learning Protein Binding Software
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Prediction of possible new drug binding site for ATP-sensitive potassium channel inhibition: bupropion's modulation of hippocampal CA1 neuron excitability.

Neuroreport Jul 10, 2025
OBJECTIVE: Bupropion, a norepinephrine-dopamine reuptake inhibitor, is widely used as an antidepressant and smoking cessation aid. At high doses, it also inhibits pancreatic β-cell ATP-sensitive potassium (KATP) channels, inducing insulin secretion. ...
KATP Channels Binding Sites Pyramidal Cells Membrane Potentials Bupropion Patch-Clamp Techniques Action Potentials Mice, Inbred C57BL CA1 Region, Hippocampal Male Mice Animals
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AI based natural inhibitor targeting RPS20 for colorectal cancer treatment using integrated computational approaches.

Scientific reports Jul 10, 2025
The increasing global incidence of cancer emphasizes the vital role of machine learning algorithms and artificial intelligence (AI) in identifying novel anticancer targets and developing new drugs. Computational approaches can significantly quicken r...
Artificial Intelligence Machine Learning Colorectal Neoplasms Humans Indoles Binding Sites Ribosomal Proteins Molecular Docking Simulation Antineoplastic Agents Molecular Dynamics Simulation
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Machine learning-based QSAR and structure-based virtual screening guided discovery of novel mIDH1 inhibitors from natural products.

Journal of computer-aided molecular design Jul 8, 2025
Mutations in isocitrate dehydrogenase 1 (IDH1) have been widely observed in various tumors, such as gliomas and acute myeloid leukemia, and therefore has become one of the current research focal points. Therefore, it is crucial to find inhibitors tha...
Binding Sites Biological Products Ligands Molecular Docking Simulation Humans Enzyme Inhibitors Drug Discovery Machine Learning Quantitative Structure-Activity Relationship Protein Binding Isocitrate Dehydrogenase
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