AIMC Topic: Bacterial Proteins

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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...
Bacterial Proteins Protein Conformation Cross-Linking Reagents Mass Spectrometry Models, Molecular Iron Deep Learning Bacillus subtilis
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DeepPhoPred: Accurate Deep Learning Model to Predict Microbial Phosphorylation.

Proteins Sep 6, 2024
Phosphorylation is a substantial posttranslational modification of proteins that refers to adding a phosphate group to the amino acid side chain after translation process in the ribosome. It is vital to coordinate cellular functions, such as regulati...
Bacterial Proteins Phosphoproteins Serine Protein Processing, Post-Translational Databases, Protein Phosphorylation Threonine Neural Networks, Computer Software Deep Learning Computational Biology
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Accurate prediction of antimicrobial resistance and genetic marker of Staphylococcus aureus clinical isolates using MALDI-TOF MS and machine learning - across DRIAMS and Taiwan database.

International journal of antimicrobial agents Sep 6, 2024
BACKGROUND: The use of matrix-assisted laser desorption/ionisation-time-of-flight mass spectra (MALDI-TOF MS) with machine learning (ML) has been explored for predicting antimicrobial resistance. This study evaluates the effectiveness of MALDI-TOF MS...
Drug Resistance, Bacterial Databases, Factual Microbial Sensitivity Tests Humans Machine Learning Anti-Bacterial Agents Penicillin-Binding Proteins Oxacillin Genetic Markers Staphylococcal Infections Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Staphylococcus aureus Taiwan Bacterial Proteins
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Characterizing Secretion System Effector Proteins With Structure-Aware Graph Neural Networks and Pre-Trained Language Models.

IEEE journal of biomedical and health informatics Sep 5, 2024
The Type III Secretion Systems (T3SSs) play a pivotal role in host-pathogen interactions by mediating the secretion of type III secretion system effectors (T3SEs) into host cells. These T3SEs mimic host cell protein functions, influencing interaction...
Computational Biology Bacterial Proteins Type III Secretion Systems Humans Neural Networks, Computer
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Classification of subspecies based on MALDI-TOF MS protein profiles using machine learning models.

Microbiology spectrum Aug 20, 2024
UNLABELLED: is an important bacterial species used as a starter culture for fermented foods; however, two subspecies within this species exhibit different properties in the foods. Matrix-assisted laser desorption/ionization-time of flight mass spect...
Machine Learning Bacterial Typing Techniques Support Vector Machine Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Food Microbiology Bacterial Proteins Fermented Foods Latilactobacillus sakei
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Integrated structural proteomics and machine learning-guided mapping of a highly protective precision vaccine against mycoplasma pulmonis.

International immunopharmacology Aug 16, 2024
Mycoplasma pulmonis (M. pulmonis) is an emerging respiratory infection commonly linked to prostate cancer, and it is classified under the group of mycoplasmas. Improved management of mycoplasma infections is essential due to the frequent ineffectiven...
Bacterial Vaccines Epitope Mapping T-Lymphocytes, Cytotoxic Mycoplasma Infections Bacterial Proteins Antigens, Bacterial Epitopes, B-Lymphocyte Mice Proteomics Humans Machine Learning Animals Epitopes, T-Lymphocyte Molecular Docking Simulation
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Modelling the rapid detection of Carbapenemase-resistant Klebsiella pneumoniae based on machine learning and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Diagnostic microbiology and infectious disease Jul 30, 2024
In this study, 80 carbapenem-resistant Klebsiella pneumoniae (CR-KP) and 160 carbapenem-susceptible Klebsiella pneumoniae (CS-KP) strains detected in the clinic were selected and their matrix-assisted laser desorption/ionization time-of-flight mass s...
ROC Curve Carbapenem-Resistant Enterobacteriaceae Klebsiella pneumoniae Anti-Bacterial Agents Bacterial Proteins Klebsiella Infections Humans Sensitivity and Specificity beta-Lactamases Machine Learning Microbial Sensitivity Tests Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Identification of key drivers of antimicrobial resistance in using machine learning.

Canadian journal of microbiology Jul 30, 2024
With antimicrobial resistance (AMR) rapidly evolving in pathogens, quick and accurate identification of genetic determinants of phenotypic resistance is essential for improving surveillance, stewardship, and clinical mitigation. Machine learning (ML)...
Enterococcus faecium Plasmids Gram-Positive Bacterial Infections Genome, Bacterial Microbial Sensitivity Tests Bacterial Proteins Enterococcus faecalis Machine Learning Anti-Bacterial Agents Drug Resistance, Bacterial Humans
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Neural network extrapolation to distant regions of the protein fitness landscape.

Nature communications Jul 30, 2024
Machine learning (ML) has transformed protein engineering by constructing models of the underlying sequence-function landscape to accelerate the discovery of new biomolecules. ML-guided protein design requires models, trained on local sequence-functi...
Immunoglobulin G Protein Binding Models, Molecular Neural Networks, Computer Machine Learning Bacterial Proteins Protein Engineering
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Identification of novel toxins associated with the extracellular contractile injection system using machine learning.

Molecular systems biology Jul 28, 2024
Secretion systems play a crucial role in microbe-microbe or host-microbe interactions. Among these systems, the extracellular contractile injection system (eCIS) is a unique bacterial and archaeal extracellular secretion system that injects protein t...
Humans Machine Learning Bacterial Proteins Bacterial Toxins
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