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Molecular Docking Simulation

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Deciphering the Pharmacological Potential of Kouqiangjie Formula for the Treatment of Diabetic Periodontitis Based on Network Pharmacology, Machine Learning, Molecular Dynamics, and Animal Experiments.

Drug design, development and therapy
BACKGROUND: Periodontitis (PD) and type 2 diabetes mellitus (T2DM) represent interlinked global health burdens, commonly causing significant clinical complications when coincident. Therefore, managing both conditions (T2DM with periodontitis, DP) sim...

DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning.

Nucleic acids research
Ribonucleic Acid (RNA) is the central conduit for information transfer in the cell. Identifying potential RNA targets in disease conditions is a challenging task, given the vast repertoire of functional non-coding RNAs in a human cell. A potential dr...

In silico discovery of novel compounds for FAK activation using virtual screening, AI-based prediction, and molecular dynamics.

Computational biology and chemistry
Focal Adhesion Kinase (FAK) is a non-receptor tyrosine kinase that plays a crucial role in cell proliferation, migration, and signal transduction. FAK is overexpressed in metastatic and advanced-stage cancers, where it is considered a key kinase in c...

Artificial Intelligence: A New Tool for Structure-Based G Protein-Coupled Receptor Drug Discovery.

Biomolecules
Understanding protein structures can facilitate the development of therapeutic drugs. Traditionally, protein structures have been determined through experimental approaches such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy...

AI-augmented physics-based docking for antibody-antigen complex prediction.

Bioinformatics (Oxford, England)
MOTIVATION: Predicting the structure of antibody-antigen complexes is a challenging task with significant implications for the design of better antibody therapeutics. However, the levels of success have remained dauntingly low, particularly when high...

Pan-cancer analysis of CDC7 in human tumors: Integrative multi-omics insights and discovery of novel marine-based inhibitors through machine learning and computational approaches.

Computers in biology and medicine
Cancer remains a significant global health challenge, with the Cell Division Cycle 7 (CDC7) protein emerging as a potential therapeutic target due to its critical role in tumor proliferation, survival, and resistance. However, a comprehensive analysi...

RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning.

Nature communications
RNAs are a vast reservoir of untapped drug targets. Structure-based virtual screening (VS) identifies candidate molecules by leveraging binding site information, traditionally using molecular docking simulations. However, docking struggles to scale w...

Integrating single-cell RNA sequencing, WGCNA, and machine learning to identify key biomarkers in hepatocellular carcinoma.

Scientific reports
The microarray and single-cell RNA-sequencing (scRNA-seq) datasets of hepatocellular carcinoma (HCC) were downloaded from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis (W...

Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds?

Journal of chemical information and modeling
Allosteric compounds offer an alternative mode of inhibition to orthosteric compounds with opportunities for selectivity and noncompetition. Structure-based drug design (SBDD) of allosteric compounds introduces complications compared to their orthost...