AIMC Topic: Protein Conformation

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The Development of Target-Specific Machine Learning Models as Scoring Functions for Docking-Based Target Prediction.

Journal of chemical information and modeling Mar 18, 2019
The identification of possible targets for a known bioactive compound is of the utmost importance for drug design and development. Molecular docking is one possible approach for in-silico protein target prediction, whereas a molecule is docked into s...
Molecular Docking Simulation Computational Biology Support Vector Machine Protein Conformation Neural Networks, Computer Machine Learning
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Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis.

Journal of the American Chemical Society Feb 21, 2019
Despite tremendous progress in understanding and engineering enzymes, knowledge of how enzyme structures and their dynamics induce observed catalytic properties is incomplete, and capabilities to engineer enzymes fall far short of industrial needs. H...
Protein Conformation Monte Carlo Method Substrate Specificity Machine Learning Molecular Dynamics Simulation Biocatalysis Ketol-Acid Reductoisomerase
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PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine.

BMC bioinformatics Dec 31, 2018
BACKGROUND: Identifying specific residues for protein-DNA interactions are of considerable importance to better recognize the binding mechanism of protein-DNA complexes. Despite the fact that many computational DNA-binding residue prediction approach...
Humans Machine Learning Algorithms Protein Binding Computational Biology DNA-Binding Proteins Support Vector Machine Protein Conformation DNA Binding Sites
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Albumin binding, anticancer and antibacterial properties of synthesized zero valent iron nanoparticles.

International journal of nanomedicine Dec 28, 2018
BACKGROUND: Nanoparticles (NPs) have been emerging as potential players in modern medicine with clinical applications ranging from therapeutic purposes to antimicrobial agents. However, before applications in medical agents, some in vitro studies sho...
Cell Proliferation Tumor Cells, Cultured Humans Escherichia coli Anti-Bacterial Agents Metal Nanoparticles Protein Conformation Staphylococcus aureus Molecular Docking Simulation Iron Neuroblastoma Antineoplastic Agents Pseudomonas aeruginosa Serum Albumin, Human Bacteria
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Gene ontology improves template selection in comparative protein docking.

Proteins Dec 27, 2018
Structural characterization of protein-protein interactions is essential for our ability to study life processes at the molecular level. Computational modeling of protein complexes (protein docking) is important as the source of their structure and a...
Humans Software Molecular Docking Simulation Proteins Databases, Protein Models, Molecular Protein Interaction Maps Protein Binding Computational Biology Protein Interaction Mapping Structural Homology, Protein Protein Conformation Gene Ontology Binding Sites
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Rapid and specific detection of Salmonella infections using chemically modified nucleic acid probes.

Analytica chimica acta Dec 21, 2018
Salmonella is a leading source of bacterial foodborne illness in humans, causing gastroenteritis outbreaks with bacteraemia occurrences that can lead to clinical complications and death. Eggs, poultry and pig products are considered as the main carri...
Protein Conformation Models, Molecular Salmonella Oligonucleotide Probes Deoxyribonucleases Limit of Detection Time Factors Nucleic Acid Conformation Food Safety Food Microbiology
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Practical Model Selection for Prospective Virtual Screening.

Journal of chemical information and modeling Dec 18, 2018
Virtual (computational) high-throughput screening provides a strategy for prioritizing compounds for experimental screens, but the choice of virtual screening algorithm depends on the data set and evaluation strategy. We consider a wide range of liga...
Algorithms Molecular Docking Simulation User-Computer Interface Proteins Machine Learning Drug Evaluation, Preclinical Protein Conformation
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Predicting drug-target interactions using Lasso with random forest based on evolutionary information and chemical structure.

Genomics Dec 11, 2018
The identification of drug-target interactions has great significance for pharmaceutical scientific research. Since traditional experimental methods identifying drug-target interactions is costly and time-consuming, the use of machine learning method...
Ion Channels Position-Specific Scoring Matrices Machine Learning Software Drug Development Protein Conformation Databases, Protein Receptors, Cytoplasmic and Nuclear Receptors, G-Protein-Coupled
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Combined molecular dynamics and neural network method for predicting protein antifreeze activity.

Proceedings of the National Academy of Sciences of the United States of America Dec 7, 2018
Antifreeze proteins (AFPs) are a diverse class of proteins that depress the kinetically observable freezing point of water. AFPs have been of scientific interest for decades, but the lack of an accurate model for predicting AFP activity has hindered ...
Protein Conformation Thermodynamics Antifreeze Proteins Water Models, Theoretical Kinetics Molecular Dynamics Simulation Crystallization Freezing Neural Networks, Computer Temperature Animals Humans
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Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits.

Journal of computational chemistry Oct 11, 2018
We present a molecular dynamics simulation study of alkali metal cation transport through the double-helical and the head-to-head conformers of the gramicidin ion channel. Our approach is based on a thermodynamic integration network, which consists o...
Thermodynamics Ion Channels Least-Squares Analysis Molecular Dynamics Simulation Protein Conformation Neural Networks, Computer Ion Transport
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