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Binding Sites

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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...
Humans Neural Networks, Computer Algorithms Databases, Factual Protein Binding Models, Theoretical Drug Development Models, Molecular Biomarkers Drug Discovery Deep Learning Ligands Binding Sites
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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...
Peptides Neural Networks, Computer Protein Binding Proteins Binding Sites
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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...
Vitamin D 25-Hydroxyvitamin D3 1-alpha-Hydroxylase Structure-Activity Relationship Metabolic Networks and Pathways Drug Design Humans Protein Binding Support Vector Machine Binding Sites Neural Networks, Computer Small Molecule Libraries Machine Learning Databases, Pharmaceutical Phosphotransferases Models, Molecular Algorithms Molecular Dynamics Simulation Reproducibility of Results Amino Acid Sequence Animals Enzyme Inhibitors Molecular Docking 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...
Quantitative Structure-Activity Relationship Protein Kinase Inhibitors Binding Sites Proto-Oncogene Proteins c-abl Machine Learning Molecular Structure Molecular Docking Simulation Molecular Dynamics Simulation Drug Design Ligands Protein Binding Humans
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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...
Machine Learning Molecular Docking Simulation Drug Discovery ROC Curve Protein Binding Structure-Activity Relationship Models, Molecular Class Ib Phosphatidylinositol 3-Kinase Molecular Structure Molecular Conformation Molecular Dynamics Simulation Binding Sites Ligands Phosphoinositide-3 Kinase Inhibitors Databases, Pharmaceutical
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Machine learning differentiates enzymatic and non-enzymatic metals in proteins.

Nature communications Jun 17, 2021
Metalloenzymes are 40% of all enzymes and can perform all seven classes of enzyme reactions. Because of the physicochemical similarities between the active sites of metalloenzymes and inactive metal binding sites, it is challenging to differentiate b...
Enzymes Metalloproteins Catalytic Domain Machine Learning Static Electricity Metals Algorithms Binding Sites Databases, Protein Models, Molecular Catalysis
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Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2.

The journal of physical chemistry letters Jun 4, 2021
SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine lear...
Spike Glycoprotein, Coronavirus Models, Molecular Molecular Dynamics Simulation Angiotensin-Converting Enzyme 2 Binding Sites Humans Machine Learning
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Convolutional neural networks (CNNs): concepts and applications in pharmacogenomics.

Molecular diversity May 24, 2021
Convolutional neural networks (CNNs) have been used to extract information from various datasets of different dimensions. This approach has led to accurate interpretations in several subfields of biological research, like pharmacogenomics, addressing...
Drug Development Neural Networks, Computer DNA Artificial Intelligence Drug Interactions Data Analysis RNA Precision Medicine Pharmacogenetics Polymorphism, Single Nucleotide Binding Sites Regulatory Sequences, Nucleic Acid
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DeepD2V: A Novel Deep Learning-Based Framework for Predicting Transcription Factor Binding Sites from Combined DNA Sequence.

International journal of molecular sciences May 24, 2021
Predicting in vivo protein-DNA binding sites is a challenging but pressing task in a variety of fields like drug design and development. Most promoters contain a number of transcription factor (TF) binding sites, but only a small minority has been id...
Computational Biology Binding Sites Humans Transcription Factors Software Cell Line Deep Learning DNA-Binding Proteins DNA Promoter Regions, Genetic K562 Cells
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