AIMC Topic: Molecular Docking Simulation

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Identifying toxicological effects of perfluoroalkyl and polyfluoroalkyl substances exposure on osteoarthritis.

Scientific reports
Perfluoroalkyl and polyfluoroalkyl substances (PFAS) pose a significant challenge due to their persistence, bioaccumulation, and multi-system toxicity. Their impact on degenerative diseases, particularly osteoarthritis (OA), remains understudied, nec...

A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein-Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases.

Journal of chemical information and modeling
The accurate prediction of protein-ligand binding poses and affinities is central to structure-based drug design. In this study, we first benchmarked three distinct pose generation strategies for data sets from the ASAP Antiviral Challenge 2025: mole...

In silico-driven protocol for hit-to-lead optimization: a case study on PDE9A inhibitors.

Journal of computer-aided molecular design
Hit-to-lead (H2L) optimization is a critical stage in small-molecule drug discovery, where efficient exploration of chemical space is required to identify promising lead compounds. Conventional H2L workflows rely on iterative synthesis and experiment...

Revealing the anti-tumor mechanisms of aromatic oil from Amomum villosum through integrated network pharmacology, bioinformatics, machine learning, single-cell sequencing, and cell experiments.

Biochemical and biophysical research communications
The dry fruits of Amomum villosum (Av) are a traditional Chinese medicine used for gastrointestinal disease. Aromatic oil has been reported to have anti-tumor properties. However, its therapeutic potential and molecular mechanisms remain unclear. Int...

An evaluation of Roluperidone as a promising repurposing candidate for Alzheimer's Disease: A Computational Investigation.

PloS one
Alzheimer's disease (AD) is the most dominant and prevalent form of dementia. The therapeutic agents for AD are not sufficient. Drug repurposing (i.e., also called drug repositioning or therapeutic switching of drugs) could contribute to adding novel...

Exploring shared diagnostic genes and molecular mechanisms in multiple sclerosis and psoriasis through bioinformatics analysis and machine learning.

Biochemical and biophysical research communications
BACKGROUND: Multiple sclerosis (MS) and psoriasis are both immune-mediated inflammatory diseases. Previous studies have reported comorbidity between MS and psoriasis, but the underlying mechanisms remain unclear. This study aims to elucidate the shar...

Discovery of Tetrahydroisoquinoline-Based SARS-CoV-2 Helicase Inhibitors with Iterative, Deep Learning-Enhanced Virtual Screening.

Journal of chemical information and modeling
In this study, we pursued a structure-based drug discovery campaign targeting the SARS-CoV-2 helicase through three rounds of virtual screening (VS) enhanced with Artificial Intelligence (AI). The third round incorporated a deep neural network (DNN) ...

Unveiling potent xanthine oxidase inhibitors in two Balanophora spp. using machine learning-based virtual screening and molecular docking approach.

Scientific reports
Pharmacological studies revealed that the Balanophora species contains diverse phytochemicals which enable interesting biological activities and emphasize their pharmaceutical relevance. Previously, we identified significant xanthine oxidase (XO) inh...

Machine learning-guided identification and simulation-based validation of potent JAK3 inhibitors for cancer therapy.

PloS one
Janus kinase 3 (JAK3) is a hematopoietic-specific kinase implicated in cytokine signaling and immune dysregulation and has recently been associated with cancer progression. However, selective and potent JAK3 inhibitors remain underdeveloped. In this ...

Combining Retip Retention Time Prediction with High-Resolution Mass Spectrometry: A Systematic Analysis of - Conducted for the First Time.

Analytical chemistry
- Herbal Pair (SEHP) is one of the classic Chinese herbal formulas for treating Alzheimer's disease (AD), but its complex chemical composition renders traditional analytical methods inefficient. Retention time (RT) provides complementary information ...