AIMC Topic: Binding Sites

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The prediction of RNA-small-molecule ligand binding affinity based on geometric deep learning.

Computational biology and chemistry Jan 29, 2025
Small molecule-targeted RNA is an emerging technology that plays a pivotal role in drug discovery and inhibitor design, with widespread applications in disease treatment. Consequently, predicting RNA-small-molecule ligand interactions is crucial. Wit...
Small Molecule Libraries Deep Learning Ligands RNA Binding Sites
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MutualDTA: An Interpretable Drug-Target Affinity Prediction Model Leveraging Pretrained Models and Mutual Attention.

Journal of chemical information and modeling Jan 29, 2025
Efficient and accurate drug-target affinity (DTA) prediction can significantly accelerate the drug development process. Recently, deep learning models have been widely applied to DTA prediction and have achieved notable success. However, existing met...
Humans Proteins Drug Discovery Pharmaceutical Preparations Binding Sites Deep Learning Protein Binding
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MAI-TargetFisher: A proteome-wide drug target prediction method synergetically enhanced by artificial intelligence and physical modeling.

Acta pharmacologica Sinica Jan 27, 2025
Computational target identification plays a pivotal role in the drug development process. With the significant advancements of deep learning methods for protein structure prediction, the structural coverage of human proteome has increased substantial...
Proteins Databases, Protein Binding Sites Algorithms Drug Discovery Proteome Humans Artificial Intelligence
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DisDock: A Deep Learning Method for Metal Ion-Protein Redocking.

Proteins Jan 22, 2025
The structures of metalloproteins are essential for comprehending their functions and interactions. The breakthrough of AlphaFold has made it possible to predict protein structures with experimental accuracy. However, the type of metal ion that a met...
Databases, Protein Ions Ligands Protein Binding Computational Biology Metalloproteins Protein Conformation Binding Sites Software Algorithms Deep Learning Metals Molecular Docking Simulation
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MVGNN-PPIS: A novel multi-view graph neural network for protein-protein interaction sites prediction based on Alphafold3-predicted structures and transfer learning.

International journal of biological macromolecules Jan 21, 2025
Protein-protein interactions (PPI) are crucial for understanding numerous biological processes and pathogenic mechanisms. Identifying interaction sites is essential for biomedical research and targeted drug development. Compared to experimental metho...
Binding Sites Protein Interaction Mapping Graph Neural Networks Models, Molecular Protein Conformation Neural Networks, Computer Algorithms Computational Biology Proteins Protein Binding
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MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction.

Journal of chemical information and modeling Jan 20, 2025
Predicting drug-target binding affinity (DTA) is a crucial task in drug discovery research. Recent studies have demonstrated that pocket features and interactions between targets and drugs significantly improve the understanding of DTA. However, chal...
Humans Drug Discovery Proteins Pharmaceutical Preparations Deep Learning Binding Sites Protein Binding
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Identifying Protein-Nucleotide Binding Residues via Grouped Multi-task Learning and Pre-trained Protein Language Models.

Journal of chemical information and modeling Jan 9, 2025
The accurate identification of protein-nucleotide binding residues is crucial for protein function annotation and drug discovery. Numerous computational methods have been proposed to predict these binding residues, achieving remarkable performance. H...
Binding Sites Deep Learning Protein Binding Databases, Protein Nucleotides Proteins
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ProPr54 web server: predicting σ promoters and regulon with a hybrid convolutional and recurrent deep neural network.

NAR genomics and bioinformatics Jan 7, 2025
σ serves as an unconventional sigma factor with a distinct mechanism of transcription initiation, which depends on the involvement of a transcription activator. This unique sigma factor σ is indispensable for orchestrating the transcription of genes ...
Software Bacterial Proteins Internet Neural Networks, Computer Sigma Factor Regulon RNA Polymerase Sigma 54 Binding Sites Genome, Bacterial Promoter Regions, Genetic
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Deep Learning Approaches for the Prediction of Protein Functional Sites.

Molecules (Basel, Switzerland) Jan 7, 2025
Knowing which residues of a protein are important for its function is of paramount importance for understanding the molecular basis of this function and devising ways of modifying it for medical or biotechnological applications. Due to the difficulty...
Humans Deep Learning Databases, Protein Computational Biology Binding Sites Proteins Sequence Analysis, Protein
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PharmRL: pharmacophore elucidation with deep geometric reinforcement learning.

BMC biology Dec 31, 2024
BACKGROUND: Molecular interactions between proteins and their ligands are important for drug design. A pharmacophore consists of favorable molecular interactions in a protein binding site and can be utilized for virtual screening. Pharmacophores are ...
Ligands Drug Design Pharmacophore Binding Sites Humans Deep Learning Algorithms Proteins
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