AIMC Topic: Protein Binding

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MCN-CPI: Multiscale Convolutional Network for Compound-Protein Interaction Prediction.

Biomolecules Jul 29, 2021
In the process of drug discovery, identifying the interaction between the protein and the novel compound plays an important role. With the development of technology, deep learning methods have shown excellent performance in various situations. Howeve...
Protein Conformation, beta-Strand Drugs, Investigational Binding Sites Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Molecular Docking Simulation Drug Discovery Deep Learning Protein Binding Proteins Kinetics High-Throughput Screening Assays Datasets as Topic Humans
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Deep learning-based prediction of TFBSs in plants.

Trends in plant science Jul 24, 2021
Computational Biology Transcription Factors Binding Sites Deep Learning 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...
Protein Binding Models, Theoretical Drug Development Models, Molecular Biomarkers Drug Discovery Deep Learning Ligands Binding Sites Humans Neural Networks, Computer Algorithms Databases, Factual
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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...
Protein Binding Proteins Binding Sites Neural Networks, Computer Peptides
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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 Binding Sites Small Molecule Libraries Databases, Pharmaceutical Phosphotransferases Protein Binding Reproducibility of Results 25-Hydroxyvitamin D3 1-alpha-Hydroxylase Molecular Dynamics Simulation Support Vector Machine Animals Structure-Activity Relationship Vitamin D Amino Acid Sequence Neural Networks, Computer Metabolic Networks and Pathways Molecular Docking Simulation Enzyme Inhibitors Machine Learning Models, Molecular Drug Design Algorithms
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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...
Ligands Glycogen Synthase Kinase 3 beta Thermodynamics Bridged-Ring Compounds Machine Learning 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...
Ligands Drug Design Humans Quantitative Structure-Activity Relationship Binding Sites Protein Binding Protein Kinase Inhibitors Machine Learning Proto-Oncogene Proteins c-abl Molecular Structure Molecular Docking Simulation Molecular Dynamics 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...
Structure-Activity Relationship Phosphoinositide-3 Kinase Inhibitors Ligands Models, Molecular Databases, Pharmaceutical Drug Discovery Molecular Conformation Machine Learning Molecular Structure Class Ib Phosphatidylinositol 3-Kinase ROC Curve Molecular Docking Simulation Binding Sites Molecular Dynamics Simulation Protein Binding
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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...
Machine Learning Amino Acid Sequence Protein Binding Proteins Mutation
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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...
Drug Design Drug Discovery Big Data Protein Binding Models, Theoretical Proteins Structure-Activity Relationship Humans Protein Interaction Mapping Models, Molecular Artificial Intelligence Protein Folding Workflow Algorithms Databases, Pharmaceutical Data Mining
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