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Protein Binding

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Logistic matrix factorisation and generative adversarial neural network-based method for predicting drug-target interactions.

Molecular diversity Jul 23, 2021
Identifying drug-target protein association pairs is a prerequisite and a crucial task in drug discovery and development. Numerous computational models, based on different assumptions and algorithms, have been proposed as an alternative to the labori...
Models, Molecular Ligands Binding Sites Protein Binding Models, Theoretical Drug Development Humans Neural Networks, Computer Algorithms Drug Discovery Deep Learning Databases, Factual Biomarkers
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Protein-Peptide Binding Site Detection Using 3D Convolutional Neural Networks.

Journal of chemical information and modeling Jul 22, 2021
Peptides and peptide-based molecules represent a promising therapeutic modality targeting intracellular protein-protein interactions, potentially combining the beneficial properties of biologics and small-molecule drugs. Protein-peptide complexes occ...
Neural Networks, Computer Binding Sites Peptides Protein Binding Proteins
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Identification of kinase inhibitors that rule out the CYP27B1-mediated activation of vitamin D: an integrated machine learning and structure-based drug designing approach.

Molecular diversity Jul 16, 2021
CYP27B1, a cytochrome P450-containing hydroxylase enzyme, converts vitamin D precursor calcidiol (25-hydroxycholecalciferol) to its active form calcitriol (1α,25(OH)D). Tyrosine kinase inhibitor such as imatinib is reported to interfere with the acti...
Humans Neural Networks, Computer Machine Learning Small Molecule Libraries Databases, Pharmaceutical Phosphotransferases Amino Acid Sequence Enzyme Inhibitors Binding Sites Algorithms Molecular Docking Simulation Reproducibility of Results Drug Design Animals Protein Binding Support Vector Machine Vitamin D Structure-Activity Relationship 25-Hydroxyvitamin D3 1-alpha-Hydroxylase Models, Molecular Metabolic Networks and Pathways Molecular Dynamics Simulation
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Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy.

Journal of chemical theory and computation Jul 14, 2021
Computational capabilities are rapidly increasing, primarily because of the availability of GPU-based architectures. This creates unprecedented simulative possibilities for the systematic and robust computation of thermodynamic observables, including...
Machine Learning Ligands Glycogen Synthase Kinase 3 beta Thermodynamics Bridged-Ring Compounds Protein Binding Imidazoles Molecular Dynamics Simulation
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Molecular insights on ABL kinase activation using tree-based machine learning models and molecular docking.

Molecular diversity Jun 30, 2021
Abelson kinase (c-Abl) is a non-receptor tyrosine kinase involved in several biological processes essential for cell differentiation, migration, proliferation, and survival. This enzyme's activation might be an alternative strategy for treating disea...
Molecular Dynamics Simulation Drug Design Proto-Oncogene Proteins c-abl Protein Kinase Inhibitors Ligands Binding Sites Humans Protein Binding Quantitative Structure-Activity Relationship Machine Learning Molecular Structure Molecular Docking Simulation
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A multi-conformational virtual screening approach based on machine learning targeting PI3Kγ.

Molecular diversity Jun 23, 2021
Nowadays, more and more attention has been attracted to develop selective PI3Kγ inhibitors, but the unique structural features of PI3Kγ protein make it a very big challenge. In the present study, a virtual screening strategy based on machine learning...
Class Ib Phosphatidylinositol 3-Kinase Protein Binding Structure-Activity Relationship Models, Molecular Molecular Docking Simulation Machine Learning Drug Discovery ROC Curve Molecular Structure Phosphoinositide-3 Kinase Inhibitors Molecular Conformation Molecular Dynamics Simulation Databases, Pharmaceutical Binding Sites Ligands
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PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures.

Journal of bioinformatics and computational biology Jun 11, 2021
Accurately determining a change in protein binding affinity upon mutations is important to find novel therapeutics and to assist mutagenesis studies. Determination of change in binding affinity upon mutations requires sophisticated, expensive, and ti...
Proteins Mutation Amino Acid Sequence Machine Learning Protein Binding
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Applications of artificial intelligence to drug design and discovery in the big data era: a comprehensive review.

Molecular diversity Jun 10, 2021
Artificial intelligence (AI) renders cutting-edge applications in diverse sectors of society. Due to substantial progress in high-performance computing, the development of superior algorithms, and the accumulation of huge biological and chemical data...
Protein Folding Humans Artificial Intelligence Databases, Pharmaceutical Algorithms Big Data Models, Molecular Drug Design Models, Theoretical Protein Binding Workflow Data Mining Drug Discovery Proteins Protein Interaction Mapping Structure-Activity Relationship
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Machine learning for profile prediction in genomics.

Current opinion in chemical biology Jun 6, 2021
A recent deluge of publicly available multi-omics data has fueled the development of machine learning methods aimed at investigating important questions in genomics. Although the motivations for these methods vary, a task that is commonly adopted is ...
Machine Learning Genome Chromatin Protein Binding Genomics
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Computational representations of protein-ligand interfaces for structure-based virtual screening.

Expert opinion on drug discovery Jun 3, 2021
: Structure-based virtual screening (SBVS) is an essential strategy for hit identification. SBVS primarily uses molecular docking, which exploits the protein-ligand binding mode and associated affinity score for compound ranking. Previous studies hav...
Protein Binding Proteins Ligands Humans Machine Learning Molecular Docking Simulation
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