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Screening of potent STAT3-SH2 domain inhibitors from JAK/STAT compound library through molecular dynamics simulation
AbstractThe Signal Transducer and Activator of Transcription 3 (STAT3) protein is activated consistently in the tumor cells and thus studied as a...
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NASA’s Ground-Based Microgravity Simulation Facility
Since opportunities to conduct experiments in space are scarce, various microgravity simulators and analogs have been widely used in space biology...
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Network pharmacology, molecular docking, and molecular dynamics simulation analysis reveal the molecular mechanism of halociline against gastric cancer
Halociline, a derivative of alkaloids, was isolated from the marine fungus Penicillium griseofulvum by our group. This remarkable compound exhibits...
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Simulation as a Form of Scientific Investigation
This volume is motivated by practical goals. In particular, it is meant to empower the reader to use computer simulation of biological populations...
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Molecular Simulation of Stapled Peptides
Constrained peptides represent a relatively new class of biologic therapeutics, which have the potential to overcome several limitations of...
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Exploration of Whole Blood Chromium as Biomarker of Hexavalent Chromium Exposure: Based on Literature Review and Monte Carlo Simulation
Hexavalent chromium (Cr(VI)) is a sort of common industrial poison and environmental pollutant posing great health threat to the population....
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Which data subset should be augmented for deep learning? a simulation study using urothelial cell carcinoma histopathology images
BackgroundApplying deep learning to digital histopathology is hindered by the scarcity of manually annotated datasets. While data augmentation can...
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Biomass Fast Pyrolysis Simulation: A Thermodynamic Equilibrium Approach
This work investigates the kinetics of fast pyrolysis of different biomasses using thermogravimetric analysis and DWSIM software. The rising energy...
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Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods
Molecular dynamics simulations have proved extremely useful in investigating the functioning of proteins with atomic-scale resolution. Many...
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Unraveling the anti-breast cancer activity of Cimicifugae rhizoma using biological network pathways and molecular dynamics simulation
Cimicifugae is a commonly used treatment for breast cancer, but the specific molecular mechanisms underlying its effectiveness remain unclear. In...
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Research on wind pressure characteristics of traditional timber buildings: a case study of the main hall of Shisi Temple
Traditional timber buildings are sensitive to wind action. Studying the wind pressure characteristics is the premise for the preventive conservation...
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Direct Interaction of Minocycline to p47phox Contributes to its Attenuation of TNF-α-Mediated Neuronal PC12 Cell Death: Experimental and Simulation Validation
Minocycline, a repurposed approved medication, shows promise in treating neurodegeneration. However, the specific pathways targeted by minocycline...
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Peptide-Membrane Docking and Molecular Dynamic Simulation of In Silico Detected Antimicrobial Peptides from Portulaca oleracea’s Transcriptome
The main issue with clinical infections is multidrug resistance to traditional antibiotics. As they are essential to innate immunity, shielding hosts...
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Tamock: simulation of habitat-specific benchmark data in metagenomics
BackgroundSimulated metagenomic reads are widely used to benchmark software and workflows for metagenome interpretation. The results of metagenomic...
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Validation of the regulations for common bean (Phaseolus vulgaris l.) cultivar recommendations by computational simulation with experimental data
The value of cultivation and use (VCU) tests are required for registration of new cultivars. The rules for conducting VCU tests were very restrictive...
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Secondary structure dependence on simulation techniques and force field parameters: from disordered to ordered proteins
Computer simulations are used for identifying the secondary structure properties of ordered and disordered proteins. However, our recent studies...
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Identification of potential flavonoid compounds as antibacterial therapeutics against Klebsiella pneumoniae infection using structure-based virtual screening and molecular dynamics simulation
Klebsiella pneumoniae , which is among the top three pathogens on WHO's priority list, is one of the gram-negative bacteria that doctors and...
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Predicting the sign of trophic effects: individual-based simulation versus loop analysis
Food web research needs to be predictive in order to support decisions system-based conservation. In order to increase predictability and...
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Optimization of Greenhouse Gas Emissions Through Simulation Modeling: Analysis and Interpretation
This chapter presents a brief review on the computational model used for the simulation and optimization of Greenhouse Gases (GHGs) for the abatement...
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Validation of catalytic site residues of Ubiquitin Specific Protease 2 (USP2) by molecular dynamic simulation and novel kinetics assay for rational drug design
Post-translational modifications of proteins such as protein ubiquitination are crucial for regulating conformation, stability and localization of...
