AIMC Topic: Bacillus subtilis
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Mechanistic Study of Protein Interaction with Natto Inhibitory Peptides Targeting Xanthine Oxidase: Insights from Machine Learning and Molecular Dynamics Simulations.
Journal of chemical information and modeling
Mar 24, 2025
Bioactive peptides from food sources offer a safe and biocompatible approach to enzyme inhibition, with potential applications in managing metabolic disorders such as hyperuricemia and gout, conditions linked to excessive xanthine oxidase activity. U...
Optimizing the production and efficacy of antimicrobial bioactive compounds from in combating multi-drug-resistant pathogens.
Frontiers in cellular and infection microbiology
Jan 6, 2025
BACKGROUND: The rise of antibiotic-resistant pathogens has intensified the search for novel antimicrobial agents. This study aimed to isolate from local soil samples and evaluate its antimicrobial properties, along with optimizing the production of ...
Spectroscopy, Fourier Transform Infrared
Culture Media
Staphylococcus aureus
Bacillus subtilis
Escherichia coli
Streptomyces
Soil Microbiology
RNA, Ribosomal, 16S
Candida albicans
Microbial Sensitivity Tests
Drug Resistance, Multiple, Bacterial
DNA, Bacterial
Anti-Bacterial Agents
Anti-Infective Agents
A Multi-Omics, Machine Learning-Aware, Genome-Wide Metabolic Model of Bacillus Subtilis Refines the Gene Expression and Cell Growth Prediction.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Sep 17, 2024
Given the extensive heterogeneity and variability, understanding cellular functions and regulatory mechanisms through the analysis of multi-omics datasets becomes extremely challenging. Here, a comprehensive modeling framework of multi-omics machine ...
Modelling protein complexes with crosslinking mass spectrometry and deep learning.
Nature communications
Sep 9, 2024
Scarcity of structural and evolutionary information on protein complexes poses a challenge to deep learning-based structure modelling. We integrate experimental distance restraints obtained by crosslinking mass spectrometry (MS) into AlphaFold-Multim...
Integrating Deep Learning and Synthetic Biology: A Co-Design Approach for Enhancing Gene Expression via N-Terminal Coding Sequences.
ACS synthetic biology
Sep 4, 2024
N-terminal coding sequence (NCS) influences gene expression by impacting the translation initiation rate. The NCS optimization problem is to find an NCS that maximizes gene expression. The problem is important in genetic engineering. However, current...
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
Jul 23, 2024
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....
Pestalotiopols E-J, Six New Polyketide Derivatives from a Marine Derived Fungus sp. SWMU-WZ04-1.
Marine drugs
Dec 26, 2023
Chemical epigenetic cultivation of the sponge-derived fungus sp. SWMU-WZ04-1 contributed to the identification of twelve polyketide derivatives, including six new pestalotiopols E-J (-) and six known analogues (-). Their gross structures were deduce...
Deep protein representations enable recombinant protein expression prediction.
Computational biology and chemistry
Oct 27, 2021
A crucial process in the production of industrial enzymes is recombinant gene expression, which aims to induce enzyme overexpression of the genes in a host microbe. Current approaches for securing overexpression rely on molecular tools such as adjust...
Antibiofilm Activity of α-Amylase from Bacillus subtilis and Prediction of the Optimized Conditions for Biofilm Removal by Response Surface Methodology (RSM) and Artificial Neural Network (ANN).
Applied biochemistry and biotechnology
Mar 1, 2021
α-amylase is known to have antibiofilm activity against biofilms of both Gram positive and Gram-negative bacterial strains. Partially purified α-amylase from Bacillus subtilis was found to have inhibit biofilm formed by P. aeruginosa and S. aureus. T...
Detecting operons in bacterial genomes via visual representation learning.
Scientific reports
Jan 22, 2021
Contiguous genes in prokaryotes are often arranged into operons. Detecting operons plays a critical role in inferring gene functionality and regulatory networks. Human experts annotate operons by visually inspecting gene neighborhoods across pileups ...
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