AIMC Topic: Molecular Dynamics Simulation

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Support Vector Machine as a Supervised Learning for the Prioritization of Novel Potential SARS-CoV-2 Main Protease Inhibitors.

International journal of molecular sciences Jul 19, 2021
In the last year, the COVID-19 pandemic has highly affected the lifestyle of the world population, encouraging the scientific community towards a great effort on studying the infection molecular mechanisms. Several vaccine formulations are nowadays a...
COVID-19 SARS-CoV-2 Molecular Docking Simulation Antiviral Agents Humans Pandemics COVID-19 Drug Treatment Viral Nonstructural Proteins Small Molecule Libraries Databases, Pharmaceutical Support Vector Machine Molecular Dynamics Simulation Drug Evaluation, Preclinical Supervised Machine Learning Coronavirus Protease Inhibitors Viral Proteases
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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...
Binding Sites Small Molecule Libraries Databases, Pharmaceutical Phosphotransferases Models, Molecular Molecular Dynamics Simulation Amino Acid Sequence Enzyme Inhibitors Molecular Docking Simulation Drug Design Protein Binding Support Vector Machine Vitamin D 25-Hydroxyvitamin D3 1-alpha-Hydroxylase Structure-Activity Relationship Metabolic Networks and Pathways Machine Learning Algorithms Reproducibility of Results Humans Animals Neural Networks, Computer
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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...
Binding Sites Proto-Oncogene Proteins c-abl Molecular Dynamics Simulation Ligands Quantitative Structure-Activity Relationship Molecular Docking Simulation Humans Protein Kinase Inhibitors Drug Design Machine Learning Protein Binding Molecular Structure
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Physics-based protein structure refinement in the era of artificial intelligence.

Proteins Jun 29, 2021
Protein structure refinement is the last step in protein structure prediction pipelines. Physics-based refinement via molecular dynamics (MD) simulations has made significant progress during recent years. During CASP14, we tested a new refinement pro...
Physical Phenomena Artificial Intelligence Software Computational Biology Proteins Molecular Dynamics Simulation Markov Chains Protein Conformation
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An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19.

BioMed research international Jun 24, 2021
The recent outbreak of the deadly coronavirus disease 19 (COVID-19) pandemic poses serious health concerns around the world. The lack of approved drugs or vaccines continues to be a challenge and further necessitates the discovery of new therapeutic ...
Molecular Dynamics Simulation Molecular Docking Simulation Humans COVID-19 Drug Treatment Drug Design Artificial Intelligence Drug Discovery SARS-CoV-2 Antiviral Agents
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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...
Databases, Pharmaceutical Class Ib Phosphatidylinositol 3-Kinase Machine Learning Molecular Conformation Molecular Docking Simulation Binding Sites Models, Molecular Drug Discovery Phosphoinositide-3 Kinase Inhibitors Molecular Structure ROC Curve Molecular Dynamics Simulation Protein Binding Ligands Structure-Activity Relationship
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Discovery of novel DGAT1 inhibitors by combination of machine learning methods, pharmacophore model and 3D-QSAR model.

Molecular diversity Jun 23, 2021
DGAT1 plays a crucial controlling role in triglyceride biosynthetic pathways, which makes it an attractive therapeutic target for obesity. Thus, development of DGAT1 inhibitors with novel chemical scaffolds is desired and important in the drug discov...
Algorithms Reproducibility of Results Molecular Docking Simulation Drug Discovery ROC Curve Models, Molecular Molecular Structure Cheminformatics Molecular Dynamics Simulation Enzyme Inhibitors Databases, Chemical Quantitative Structure-Activity Relationship Humans Diacylglycerol O-Acyltransferase Machine Learning
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CASTELO: clustered atom subtypes aided lead optimization-a combined machine learning and molecular modeling method.

BMC bioinformatics Jun 22, 2021
BACKGROUND: Drug discovery is a multi-stage process that comprises two costly major steps: pre-clinical research and clinical trials. Among its stages, lead optimization easily consumes more than half of the pre-clinical budget. We propose a combined...
Molecular Dynamics Simulation Machine Learning Drug Discovery Cluster Analysis
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Machine learning models to select potential inhibitors of acetylcholinesterase activity from SistematX: a natural products database.

Molecular diversity Jun 16, 2021
Alzheimer's disease is the most common form of dementia, representing 60-70% of dementia cases. The enzyme acetylcholinesterase (AChE) cleaves the ester bonds in acetylcholine and plays an important role in the termination of acetylcholine activity a...
Cheminformatics Databases, Pharmaceutical Biological Products Structure-Activity Relationship Area Under Curve Models, Molecular Algorithms Workflow Molecular Docking Simulation Molecular Dynamics Simulation Drug Discovery Humans Acetylcholinesterase ROC Curve Machine Learning Cholinesterase Inhibitors
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