AIMC Topic: Molecular Dynamics Simulation

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Dynamicasome-a molecular dynamics-guided and AI-driven pathogenicity prediction catalogue for all genetic mutations.

Communications biology
Advances in genomic medicine accelerate the identification of mutations in disease-associated genes, but the pathogenicity of many mutations remains unknown, hindering their use in diagnostics and clinical decision-making. Predictive AI models are ge...

A computational study of cardiac glycosides from Vernonia amygdalina as PI3K inhibitors for targeting HER2 positive breast cancer.

Journal of computer-aided molecular design
The PI3K/Akt pathway plays a crucial role in regulating a broad network of proteins involved in the proliferation of HER2-positive breast cancer. The ethyl acetate fraction of Vernonia amygdalina, which contains cardiac glycosides, has been shown to ...

Harnessing protein language model for structure-based discovery of highly efficient and robust PET hydrolases.

Nature communications
Plastic waste, particularly polyethylene terephthalate (PET), presents significant environmental challenges, driving extensive research into enzymatic biodegradation. However, existing PET hydrolases (PETases) are limited by narrow sequence diversity...

Combination of Molecular Dynamics Simulations and Machine Learning Reveals Structural Characteristics of Stereochemistry-Specific Interdigitation of Synthetic Monomycoloyl Glycerol Analogs.

Journal of chemical information and modeling
Synthetic monomycoloyl glycerol (MMG) analogs possess robust immunostimulatory activity and are investigated as adjuvants for subunit vaccines in preclinical and clinical studies. These synthetic lipids consist of a glycerol moiety attached to a cory...

ABEEM Polarizable Force Field for PC Lipids: Parameterization and Molecular Dynamics Simulations.

Journal of chemical theory and computation
In additive force fields, the charge is a tunable parameter designed to represent average polarization effects through a mean-field average, which could not accurately respond to different environments. The polarizable force field (PFF) offers enhanc...

AI-Accelerated Identification of Novel Antimicrobial Peptides for Inhibiting .

Journal of agricultural and food chemistry
Fusarium head blight caused by threatens global wheat production, causing substantial yield reduction and mycotoxin accumulation. This study harnessed machine learning to accelerate the discovery of antifungal peptides targeting this phytopathogen. ...

Deep learning-based dipeptidyl peptidase IV inhibitor screening, experimental validation, and GaMD/LiGaMD analysis.

BMC biology
BACKGROUND: Dipeptidyl peptidase-4 (DPP4) is considered a crucial enzyme in type 2 diabetes (T2D) treatment, targeted by inhibitors due to its role in cleaving glucagon-like peptide-1 (GLP-1). In this study, a novel DPP4 inhibitor screening strategy ...

Integrative machine learning and molecular simulation approaches identify GSK3β inhibitors for neurodegenerative disease therapy.

Scientific reports
Neurodegenerative diseases (NDDs), including Alzheimer's disease (AD) and Parkinson's disease (PD), are a growing global health concern, especially among the elderly, posing significant challenges to well-being and survival. GSK3β, a serine/threonine...

In-silico guided identification and studies of potential FFAR4 agonists for type 2 diabetes mellitus therapy.

Expert opinion on drug discovery
BACKGROUND: The activation of free fatty acid receptor 4 (FFAR4) enhances insulin sensitivity and glucose uptake while mitigating inflammation. It is a promising therapeutic approach for managing type 2 diabetes mellitus (T2DM).

Multi-level evidence reveals PANK2 as a potential target of PFOA/PFOS-induced bone metabolism disruption: From network toxicology to in vitro validation.

Ecotoxicology and environmental safety
Perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) are two representative per- and polyfluoroalkyl substances (PFAS) that have attracted increasing attention due to their environmental persistence and potential health risks, while ...