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Binding Sites

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Estimating protein-ligand interactions with geometric deep learning and mixture density models.

Journal of biosciences 39618061
Understanding the interactions between a ligand and its molecular target is crucial in guiding the optimization of molecules for any drug design workflow. Multiple experimental and computational methods have been developed to better understand these...
Algorithms Binding Sites Deep Learning Drug Design Ligands Molecular Docking Simulation Neural Networks, Computer Protein Binding Protein Conformation Proteins
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Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Briefings in bioinformatics 39541188
Transcriptional factors (TFs) in bacteria play a crucial role in gene regulation by binding to specific DNA sequences, thereby assisting in the activation or repression of genes. Despite their central role, deciphering shape recognition of bacterial ...
Algorithms Bacteria Bacterial Proteins Binding Sites Computational Biology DNA DNA, Bacterial Machine Learning Nucleic Acid Conformation Protein Binding Transcription Factors
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Improving drug-target interaction prediction through dual-modality fusion with InteractNet.

Journal of bioinformatics and computational biology 39573831
In the drug discovery process, accurate prediction of drug-target interactions is crucial to accelerate the development of new drugs. However, existing methods still face many challenges in dealing with complex biomolecular interactions. To this end,...
Algorithms Binding Sites Computational Biology Databases, Protein Deep Learning Drug Discovery Humans Ligands Machine Learning Neural Networks, Computer Pharmaceutical Preparations Protein Binding Proteins
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Small Molecule Inhibitors of Topoisomerase I Identified by Machine Learning and In Vitro Assays.

International journal of molecular sciences 39596331
Tuberculosis (TB) caused by is a leading infectious cause of death globally. The treatment of patients becomes much more difficult for the increasingly common multi-drug resistant TB. Topoisomerase I is essential for the viability of and has been v...
Antitubercular Agents Binding Sites DNA Topoisomerases, Type I High-Throughput Screening Assays Humans Machine Learning Molecular Docking Simulation Mycobacterium tuberculosis Small Molecule Libraries Topoisomerase I Inhibitors
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Estimating AChE inhibitors from MCE database by machine learning and atomistic calculations.

Journal of molecular graphics & modelling 39561662
Acetylcholinesterase (AChE) is one of the most successful targets for the treatment of Alzheimer's disease (AD). Inhibition of AChE can result in preventing AD. In this context, the machine-learning (ML) model, molecular docking, and molecular dynami...
Acetylcholinesterase Binding Sites Cholinesterase Inhibitors Databases, Chemical Humans Ligands Machine Learning Molecular Docking Simulation Molecular Dynamics Simulation Protein Binding
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DeepMiRBP: a hybrid model for predicting microRNA-protein interactions based on transfer learning and cosine similarity.

BMC bioinformatics 39695955
BACKGROUND: Interactions between microRNAs and RNA-binding proteins are crucial for microRNA-mediated gene regulation and sorting. Despite their significance, the molecular mechanisms governing these interactions remain underexplored, apart from sequ...
Binding Sites Computational Biology Deep Learning MicroRNAs Neural Networks, Computer RNA-Binding Proteins
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Residue-Level Multiview Deep Learning for ATP Binding Site Prediction and Applications in Kinase Inhibitors.

Journal of chemical information and modeling 39690486
Accurate identification of adenosine triphosphate (ATP) binding sites is crucial for understanding cellular functions and advancing drug discovery, particularly in targeting kinases for cancer treatment. Existing methods face significant challenges d...
Adenosine Triphosphate Binding Sites Deep Learning Drug Discovery Humans Ligands Molecular Docking Simulation Protein Kinase Inhibitors
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Docking-Informed Machine Learning for Kinome-wide Affinity Prediction.

Journal of chemical information and modeling 39657274
Kinase inhibitors are an important class of anticancer drugs, with 80 inhibitors clinically approved and >100 in active clinical testing. Most bind competitively in the ATP-binding site, leading to challenges with selectivity for a specific kinase, r...
Binding Sites Humans Machine Learning Molecular Docking Simulation Protein Binding Protein Conformation Protein Kinase Inhibitors Protein Kinases
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ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networks.

Computers in biology and medicine 39653625
Adenosine triphosphate plays a vital role in providing energy and enabling key cellular processes through interactions with binding proteins. The increasing amount of protein sequence data necessitates computational methods for identifying binding si...
Adenosine Triphosphate Binding Sites Computational Biology Databases, Protein Humans Neural Networks, Computer Proteins
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BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data.

Nucleic acids research 39574417
BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, trai...
Binding Sites Databases, Protein Humans Internet Knowledge Bases Protein Binding Proteins Small Molecule Libraries
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