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Molecular Docking Simulation

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Machine learning-based identification and validation of immune-related biomarkers for early diagnosis and targeted therapy in diabetic retinopathy.

Gene
The early diagnosis of diabetic retinopathy (DR) is challenging, highlighting the urgent need to identify new biomarkers. Immune responses play a crucial role in DR, yet there are currently no reports of machine learning (ML) algorithms being utilize...

Towards novel small-molecule inhibitors blocking PD-1/PD-L1 pathway: From explainable machine learning models to molecular dynamics simulation.

International journal of biological macromolecules
Molecular design of small-molecule inhibitors targeting programmed cell death-1 (PD-1)/programmed cell death ligand-1 (PD-L1) pathway has been recognized as an active research area by the clinical success of cancer immunotherapy. In recent years, usi...

Integration of 3D-QSAR, molecular docking, and machine learning techniques for rational design of nicotinamide-based SIRT2 inhibitors.

Computational biology and chemistry
Selective inhibitors of sirtuin-2 (SIRT2) are increasingly recognized as potential therapeutics for cancer and neurodegenerative diseases. Derivatives of 5-((3-amidobenzyl)oxy)nicotinamides have been identified as some of the most potent and selectiv...

High-throughput and computational techniques for aptamer design.

Expert opinion on drug discovery
INTRODUCTION: Aptamers refer to short ssDNA/RNA sequences that target small molecules, proteins, or cells. Aptamers have significantly advanced diagnostic applications, including biosensors for detecting specific biomarkers, state-of-the-art imaging,...

Deep convolutional neural network-based identification and biological evaluation of MAO-B inhibitors.

International journal of biological macromolecules
Parkinson's disease (PD) is one of the most prominent motor disorder of adult-onset dementia connected to memory and other cognitive abilities. Individuals with this vicious neurodegenerative condition tend to have an elevated expression of Monoamine...

Identification of endocrine-disrupting chemicals targeting key OP-associated genes via bioinformatics and machine learning.

Ecotoxicology and environmental safety
Osteoporosis (OP), a metabolic disorder predominantly impacting postmenopausal women, has seen considerable progress in diagnosis and treatment over the past few decades. However, the intricate interplay between genetic factors and endocrine disrupto...

Deciphering Cathepsin K inhibitors: a combined QSAR, docking and MD simulation based machine learning approaches for drug design.

SAR and QSAR in environmental research
Cathepsin K (CatK), a lysosomal cysteine protease, contributes to skeletal abnormalities, heart diseases, lung inflammation, and central nervous system and immune disorders. Currently, CatK inhibitors are associated with severe adverse effects, there...

A computational and machine learning approach to identify GPR40-targeting agonists for neurodegenerative disease treatment.

PloS one
The G protein-coupled receptor 40 (GPR40) is known to exert a significant influence on neurogenesis and neurodevelopment within the central nervous system of both humans and rodents. Research findings indicate that the activation of GPR40 by an agoni...

Development of a prognostic model related to homologous recombination deficiency in glioma based on multiple machine learning.

Frontiers in immunology
BACKGROUND: Despite advances in neuro-oncology, treatments of glioma and tools for predicting the outcome of patients remain limited. The objective of this research is to construct a prognostic model for glioma using the Homologous Recombination Defi...

Recursive dynamics of GspE through machine learning enabled identification of inhibitors.

Computational biology and chemistry
Type II secretion System has been increasingly recognized as a key driver of virulence in many pathogenic bacteria including Achromobacter xylosoxidans. ATPase GspE is the powerhouse of the T2SS. It powers the entire secretion process by binding with...