AIMC Topic: Molecular Dynamics Simulation

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Study on the mechanism of action of the active ingredient of Calculus Bovis in the treatment of sepsis by integrating single-cell sequencing and machine learning.

Medicine
BACKGROUND: Sepsis, a complex inflammatory condition with high mortality rates, lacks effective treatments. This study explores the therapeutic mechanisms of Calculus Bovis in sepsis using network pharmacology and RNA sequencing.

Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence.

The Journal of chemical physics
Membrane protein folding in the viscous microenvironment of a lipid bilayer is an inherently slow process that challenges experiments and computational efforts alike. The folding kinetics is moreover associated with topological modulations of the bio...

Machine Learning-Based Discovery of a Novel Noncovalent MurA Inhibitor as an Antibacterial Agent.

Chemical biology & drug design
The bacterial cell wall is crucial for maintaining the integrity of bacterial cells. UDP-N-acetylglucosamine 1-carboxyethylene transferase (MurA) is an important enzyme involved in bacterial cell wall synthesis. Therefore, it is an important target f...

Leveraging Artificial Intelligence in GPCR Activation Studies: Computational Prediction Methods as Key Drivers of Knowledge.

Methods in molecular biology (Clifton, N.J.)
G protein-coupled receptors (GPCRs) are key molecules involved in cellular signaling and are attractive targets for pharmacological intervention. This chapter is designed to explore the range of algorithms used to predict GPCRs' activation states, wh...

Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.

The Journal of chemical physics
Molecular dynamics simulations are crucial for understanding the structural and dynamical behavior of biomolecular systems, including the impact of their environment. However, there is a gap between the time scale of these simulations and that of rea...

An Integrated Approach to Develop a Potent Vaccine Candidate Construct Against Prostate Cancer by Utilizing Machine Learning and Bioinformatics.

Cancer reports (Hoboken, N.J.)
BACKGROUND: Prostate cancer is the most common malignancy among males. Prostaglandin G/H synthase (PGHS) is an essential enzyme in the synthesis of prostaglandins, and its activation has been linked to many malignancies, including colorectal cancer.

Machine learning-enabled virtual screening indicates the anti-tuberculosis activity of aldoxorubicin and quarfloxin with verification by molecular docking, molecular dynamics simulations, and biological evaluations.

Briefings in bioinformatics
Drug resistance in Mycobacterium tuberculosis (Mtb) is a significant challenge in the control and treatment of tuberculosis, making efforts to combat the spread of this global health burden more difficult. To accelerate anti-tuberculosis drug discove...

Deep learning path-like collective variable for enhanced sampling molecular dynamics.

The Journal of chemical physics
Several enhanced sampling techniques rely on the definition of collective variables to effectively explore free energy landscapes. The existing variables that describe the progression along a reactive pathway offer an elegant solution but face a numb...

RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method.

Briefings in bioinformatics
Small molecule drugs can be used to target nucleic acids (NA) to regulate biological processes. Computational modeling methods, such as molecular docking or scoring functions, are commonly employed to facilitate drug design. However, the accuracy of ...

Peptidic Compound as DNA Binding Agent: Fragment-based Design, Machine Learning, Molecular Modeling, Synthesis, and DNA Binding Evaluation.

Protein and peptide letters
BACKGROUND: Cancer remains a global burden, with increasing mortality rates. Current cancer treatments involve controlling the transcription of malignant DNA genes, either directly or indirectly. DNA exhibits various structural forms, including the G...