AIMC Topic: Molecular Dynamics Simulation

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Recent Advances in Machine Learning Based Prediction of RNA-protein Interactions.

Protein and peptide letters Jan 1, 2019
The interactions between RNAs and proteins play critical roles in many biological processes. Therefore, characterizing these interactions becomes critical for mechanistic, biomedical, and clinical studies. Many experimental methods can be used to det...
RNA Hydrophobic and Hydrophilic Interactions RNA-Binding Proteins Molecular Dynamics Simulation Nucleic Acid Conformation Algorithms Computational Biology Machine Learning
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[An RNA Scoring Function for Tertiary Structure Prediction Based on Multi-layer Neural Networks].

Molekuliarnaia biologiia Jan 1, 2019
A good scoring function is necessary for ab inito prediction of RNA tertiary structures. In this study, we explored the power of a machine learning based approach as a scoring function. Compared with the traditional scoring functions, the present app...
Molecular Dynamics Simulation RNA Nucleic Acid Conformation Neural Networks, Computer
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Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design.

The Journal of chemical physics Aug 21, 2018
Auto-associative neural networks ("autoencoders") present a powerful nonlinear dimensionality reduction technique to mine data-driven collective variables from molecular simulation trajectories. This technique furnishes explicit and differentiable ex...
Molecular Dynamics Simulation Dipeptides Neural Networks, Computer Peptides
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Machine learning accelerates MD-based binding pose prediction between ligands and proteins.

Bioinformatics (Oxford, England) Mar 1, 2018
MOTIVATION: Fast and accurate prediction of protein-ligand binding structures is indispensable for structure-based drug design and accurate estimation of binding free energy of drug candidate molecules in drug discovery. Recently, accurate pose predi...
Machine Learning Computational Biology Proteins Molecular Dynamics Simulation Drug Discovery Protein Binding Ligands Protein Conformation
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Approaching Pharmacological Space: Events and Components.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2018
With a view to introducing the concept of pharmacological space and its potential applications in investigating and predicting the toxic mechanisms of xenobiotics, this opening chapter describes the logical relations between conformational behavior, ...
Static Electricity Molecular Conformation Quantitative Structure-Activity Relationship Drug Discovery Fuzzy Logic Molecular Dynamics Simulation Ligands Molecular Docking Simulation
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Machine Learning and Molecular Dynamics Based Insights into Mode of Actions of Insulin Degrading Enzyme Modulators.

Combinatorial chemistry & high throughput screening Jan 1, 2017
BACKGROUND: Alzheimer's disease (AD) is one of the most common lethal neurodegenerative disorders having impact on the lives of millions of people worldwide. The disease lacks effective treatment options and the unavailability of the drugs to cure th...
Insulysin Drug Discovery Molecular Dynamics Simulation Machine Learning Molecular Docking Simulation Humans
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Integrated machine learning, molecular docking and 3D-QSAR based approach for identification of potential inhibitors of trypanosomal N-myristoyltransferase.

Molecular bioSystems Nov 15, 2016
N-Myristoyltransferase (NMT) catalyzes the transfer of myristate to the amino-terminal glycine of a subset of proteins, a co-translational modification involved in trafficking substrate proteins to membrane locations, stabilization and protein-protei...
Workflow Molecular Dynamics Simulation Enzyme Inhibitors Datasets as Topic Molecular Docking Simulation Trypanocidal Agents Machine Learning Quantitative Structure-Activity Relationship Protein Binding Algorithms Binding Sites Catalytic Domain Acyltransferases Parasitic Sensitivity Tests
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Identification of Glucose-Binding Pockets in Human Serum Albumin Using Support Vector Machine and Molecular Dynamics Simulations.

IEEE/ACM transactions on computational biology and bioinformatics Jan 1, 2016
Human Serum Albumin (HSA) has been suggested to be an alternate biomarker to the existing Hemoglobin-A1c (HbA1c) marker for glycemic monitoring. Development and usage of HSA as an alternate biomarker requires the identification of glycation sites, or...
Protein Binding Molecular Dynamics Simulation Support Vector Machine Computational Biology Serum Albumin Glucose Humans Binding Sites
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A lazy learning-based QSAR classification study for screening potential histone deacetylase 8 (HDAC8) inhibitors.

SAR and QSAR in environmental research Jan 1, 2015
Histone deacetylases 8 (HDAC8) is an enzyme repressing the transcription of various genes including tumour suppressor gene and has already become a target of human cancer treatment. In an effort to facilitate the discovery of HDAC8 inhibitors, two qu...
Histone Deacetylases Molecular Dynamics Simulation Databases, Chemical Quantitative Structure-Activity Relationship Histone Deacetylase Inhibitors Principal Component Analysis Models, Chemical Machine Learning Drug Discovery
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