AIMC Topic: Bacterial Proteins

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Enhancing the synthesis efficiency of galacto-oligosaccharides of a β-galactosidase from Paenibacillus barengoltzii by engineering the active and distal sites.

Food chemistry Apr 4, 2025
Previously, a glycoside hydrolase (GH) family 2 β-galactosidase (PbBGal2A) from Paenibacillus barengoltzii is characterized for its high transglycosylation capability. Here, the cryo-electron microscopy (cryo-EM) structure of PbBGal2A was determined,...
Bacterial Proteins Molecular Dynamics Simulation Oligosaccharides Galactose Protein Engineering Paenibacillus beta-Galactosidase Biocatalysis Catalytic Domain
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deep-Sep: a deep learning-based method for fast and accurate prediction of selenoprotein genes in bacteria.

mSystems Mar 10, 2025
Selenoproteins are a special group of proteins with major roles in cellular antioxidant defense. They contain the 21st amino acid selenocysteine (Sec) in the active sites, which is encoded by an in-frame UGA codon. Compared to eukaryotes, identificat...
Genome, Bacterial Selenoproteins Deep Learning Bacteria Bacterial Proteins Algorithms
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Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens.

Biochemistry Feb 27, 2025
The increase in antimicrobial resistance presents a major challenge in treating bacterial infections, underscoring the need for innovative drug discovery approaches and novel inhibitors. Bacterial RNA polymerase (RNAP) has emerged as a crucial target...
Enzyme Inhibitors DNA-Directed RNA Polymerases Bacterial Proteins Molecular Dynamics Simulation Humans Machine Learning Anti-Bacterial Agents Drug Resistance, Bacterial Drug Design Bacteria
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Machine learning and cheminformatics-based Identification of lichen-derived compounds targeting mutant PBP4 in Staphylococcus aureus.

Molecular diversity Feb 15, 2025
Penicillin-binding protein 4 (PBP4) is essential in imparting significant β-lactam antibiotics resistance in Staphylococcus aureus (S. aureus) and the mutation R200L in PBP4 is linked to β-lactam non-susceptibility in natural strains, complicating tr...
Anti-Bacterial Agents Molecular Docking Simulation Staphylococcus aureus Lichens Bacterial Proteins Cheminformatics Mutation Penicillin-Binding Proteins Machine Learning Molecular Dynamics Simulation
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Cloning, Characterization, and Computer-Aided Evolution of a Thermostable Laccase of the DUF152 Family From Klebsiella michiganensis.

Proteins Feb 14, 2025
Bacterial laccases exhibit relatively high optimal reaction temperatures and possess a broad substrate spectrum, thereby expanding the range of potential applications for laccase enzymes. This study aims to investigate the molecular evolution of bact...
Animals Copper Amino Acid Sequence Laccase Molecular Docking Simulation RNA, Ribosomal, 16S Bacterial Proteins Binding Sites Cloning, Molecular Mutagenesis, Site-Directed Enzyme Stability Klebsiella
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SHASI-ML: a machine learning-based approach for immunogenicity prediction in vaccine development.

Frontiers in cellular and infection microbiology Feb 11, 2025
INTRODUCTION: Accurate prediction of immunogenic proteins is crucial for vaccine development and understanding host-pathogen interactions in bacterial diseases, particularly for Salmonella infections which remain a significant global health challenge...
Proteome Salmonella Vaccines Salmonella typhimurium Immunogenicity, Vaccine Bacterial Proteins Salmonella Humans Antigens, Bacterial Computational Biology Machine Learning Salmonella Infections Vaccine Development Algorithms
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Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction.

Nature communications Feb 3, 2025
Identifying and characterizing virulence proteins secreted by Gram-negative bacteria are fundamental for deciphering microbial pathogenicity as well as aiding the development of therapeutic strategies. Effector predictors utilizing pre-trained protei...
Computational Biology Salmonella typhimurium Bacterial Proteins Virulence Factors Enterohemorrhagic Escherichia coli Machine Learning
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SProtFP: a machine learning-based method for functional classification of small ORFs in prokaryotes.

NAR genomics and bioinformatics Jan 7, 2025
Small proteins (≤100 amino acids) play important roles across all life forms, ranging from unicellular bacteria to higher organisms. In this study, we have developed SProtFP which is a machine learning-based method for functional annotation of prokar...
Humans Antimicrobial Peptides Neural Networks, Computer Open Reading Frames Gastrointestinal Microbiome Machine Learning Bacterial Proteins Bacteria Molecular Sequence Annotation Computational Biology
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ProPr54 web server: predicting σ promoters and regulon with a hybrid convolutional and recurrent deep neural network.

NAR genomics and bioinformatics Jan 7, 2025
σ serves as an unconventional sigma factor with a distinct mechanism of transcription initiation, which depends on the involvement of a transcription activator. This unique sigma factor σ is indispensable for orchestrating the transcription of genes ...
Neural Networks, Computer Software Bacterial Proteins Internet Sigma Factor Promoter Regions, Genetic Regulon Binding Sites RNA Polymerase Sigma 54 Genome, Bacterial
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DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction.

Scientific reports Dec 30, 2024
Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robust de novo protein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Tradi...
Bacterial Proteins Bacteria Microbiota Software Computational Biology Gene Ontology Deep Learning Proteins
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