AIMC Topic: Molecular Docking Simulation

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Virtual-screening of xanthine oxidase inhibitory peptides: Inhibition mechanisms and prediction of activity using machine-learning.

Food chemistry
Xanthine oxidase (XO) inhibitory peptides can prevent XO-mediated hyperuricemia. Currently, QSAR about XO inhibitory peptides with different lengths remains to be enriched. Here, XO inhibitory peptides were obtained from porcine visceral proteins thr...

Cheminformatics analysis of indoleamine and tryptophan 2,3-dioxygenase inhibitors: A descriptor and fingerprint based machine learning approach to disclose selectivity measures.

Computers in biology and medicine
Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are attractive drug targets for cancer immunotherapy. After disappointing results of the epacadostat as a selective IDO inhibitor in phase III clinical trials, there is much inter...

Identification of programmed cell death-related genes and diagnostic biomarkers in endometriosis using a machine learning and Mendelian randomization approach.

Frontiers in endocrinology
BACKGROUND: Endometriosis (EM) is a prevalent gynecological disorder frequently associated with irregular menstruation and infertility. Programmed cell death (PCD) is pivotal in the pathophysiological mechanisms underlying EM. Despite this, the preci...

Combined structure-based virtual screening and machine learning approach for the identification of potential dual inhibitors of ACC and DGAT2.

International journal of biological macromolecules
Acetyl-coenzyme A carboxylase (ACC) and diacylglycerol acyltransferase 2 (DGAT2) are recognized as potential therapeutic targets for nonalcoholic fatty liver disease (NAFLD). Inhibitors targeting ACC and DGAT2 have exhibited the capacity to reduce he...

Identification of diagnostic genes and drug prediction in metabolic syndrome-associated rheumatoid arthritis by integrated bioinformatics analysis, machine learning, and molecular docking.

Frontiers in immunology
BACKGROUND: Interactions between the immune and metabolic systems may play a crucial role in the pathogenesis of metabolic syndrome-associated rheumatoid arthritis (MetS-RA). The purpose of this study was to discover candidate biomarkers for the diag...

In silico method and bioactivity evaluation to discover novel antimicrobial agents targeting FtsZ protein: Machine learning, virtual screening and antibacterial mechanism study.

Naunyn-Schmiedeberg's archives of pharmacology
This research paper utilizes a fused-in-silico approach alongside bioactivity evaluation to identify active FtsZ inhibitors for drug discovery. Initially, ROC-guided machine learning was employed to obtain almost 13182 compounds from three libraries....

Construction of a multi-tissue compound-target interaction network of Qingfei Paidu decoction in COVID-19 treatment based on deep learning and transcriptomic analysis.

Journal of bioinformatics and computational biology
The Qingfei Paidu decoction (QFPDD) is a widely acclaimed therapeutic formula employed nationwide for the clinical management of coronavirus disease 2019 (COVID-19). QFPDD exerts a synergistic therapeutic effect, characterized by its multi-component,...

Binding and sensing diverse small molecules using shape-complementary pseudocycles.

Science (New York, N.Y.)
We describe an approach for designing high-affinity small molecule-binding proteins poised for downstream sensing. We use deep learning-generated pseudocycles with repeating structural units surrounding central binding pockets with widely varying sha...

MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics.

Journal of computer-aided molecular design
Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand-protein conformational dynamics and offers significant advantages over docking and other rigid structure-based computational methods. However, setting up, running, and an...

Redefining a new frontier in alkaptonuria therapy with AI-driven drug candidate design via innovation.

Zeitschrift fur Naturforschung. C, Journal of biosciences
A rare metabolic condition called alkaptonuria (AKU) is caused by a decrease in homogentisate 1,2 dioxygenase (HGO) activity due to a mutation in homogentisate dioxygenase (HGD) gene. Homogentisic acid is a byproduct of the catabolism of tyrosine and...