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Molecular Dynamics Simulation

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Mechanism Exploration of Dietary Supplement Astaxanthin on Improving Atherosclerosis through an Integrated Strategy Encompassing Artificial Intelligence Virtual Screening and Experimental Validation.

Journal of agricultural and food chemistry
Atherosclerosis (AS) is a major and common pathological basis of ischemic intestinal infarction, myocardial infarction, stroke, renal failure, and other highly lethal and disabling diseases. Current pharmacological interventions (e.g., statins) often...

Machine learning assisted in Silico discovery and optimization of small molecule inhibitors targeting the Nipah virus glycoprotein.

Scientific reports
The Nipah virus (NiV), a lethal pathogen from the Paramyxoviridae family, presents a significant global health threat as a result of its high mortality rate and inter-human transmission. This investigation employed in silico methods that were assiste...

Machine Learning-Guided Screening and Molecular Docking for Proposing Naturally Derived Drug Candidates Against MERS-CoV 3CL Protease.

International journal of molecular sciences
In this study, we utilized machine learning techniques to identify potential inhibitors of the MERS-CoV 3CL protease. Among the models evaluated, the Random Forest (RF) algorithm exhibited the highest predictive performance, achieving an accuracy of ...

Dynamics and Machine Learning Reveal the Link between Tripeptide Sequences and Evaporation-Driven Material Properties.

Nano letters
Previous research showed that a peptide composed of three tyrosines (YYY) can turn into organic glass and cause strong adhesion between substrates via evaporation. However, the mechanisms of these processes remain unclear, and the exploration of appl...

Unveiling Berberine analogues as potential inhibitors of Escherichia coli FtsZ through machine learning molecular docking and molecular dynamics approach.

Scientific reports
The bacterial cell division protein FtsZ, a crucial GTPase, plays a vital role in the formation of the contractile Z-ring, which is essential for bacterial cytokinesis. Consequently, inhibiting FtsZ could prevent the formation of proto-filaments and ...

Modeling Enzyme Reaction and Mutation by Direct Machine Learning/Molecular Mechanics Simulations.

Journal of chemical theory and computation
Accurately modeling enzyme reactions through direct machine learning/molecular mechanics simulations remains challenging in describing the electrostatic coupling between the QM and MM subsystems. In this work, we proposed a reweighting ME (mechanic e...

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.

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning.

PLoS computational biology
The design of proteins capable effectively binding to specific protein targets is crucial for developing therapies, diagnostics, and vaccine candidates for viral infections. Here, we introduce a complementarity-determining region (CDR) grafting appro...

Bioactive structures for inhibitors of polymerase enzyme by artificial intelligence.

Future medicinal chemistry
AIMS: Present new bioactive compounds, created by De novo Drug Design and artificial intelligence (AI), as possible inhibitors of polymerase.

A deep learning and molecular modeling approach to repurposing Cangrelor as a potential inhibitor of Nipah virus.

Scientific reports
Deforestation, urbanization, and climate change have significantly increased the risk of zoonotic diseases. Nipah virus (NiV) of Paramyxoviridae family and Henipavirus genus is transmitted by Pteropus bats. Climate-induced changes in bat migration pa...