AIMC Topic: Bacterial Proteins
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AI-based automated construction of high-precision Geobacillus thermoglucosidasius enzyme constraint model.
Metabolic engineering
Oct 18, 2024
Geobacillus thermoglucosidasius NCIMB 11955 possesses advantages, such as high-temperature tolerance, rapid growth rate, and low contamination risk. Additionally, it features efficient gene editing tools, making it one of the most promising next-gene...
Predicting photosynthetic bacteria-derived protein synthesis from wastewater using machine learning and causal inference.
Bioresource technology
Oct 15, 2024
Causal inference-assisted machine learning was used to predict photosynthetic bacterial (PSB) protein production capacity and identify key factors. The extreme gradient boosting algorithm effectively predicted protein content, while the gradient boos...
Protein interactions in human pathogens revealed through deep learning.
Nature microbiology
Sep 18, 2024
Identification of bacterial protein-protein interactions and predicting the structures of these complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here we developed RoseTTAFold2-Lit...
Machine learning reveals the transcriptional regulatory network and circadian dynamics of PCC 7942.
Proceedings of the National Academy of Sciences of the United States of America
Sep 13, 2024
is an important cyanobacterium that serves as a versatile and robust model for studying circadian biology and photosynthetic metabolism. Its transcriptional regulatory network (TRN) is of fundamental interest, as it orchestrates the cell's adaptatio...
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...
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...
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...
Penicillin-Binding Proteins
Oxacillin
Genetic Markers
Staphylococcal Infections
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Drug Resistance, Bacterial
Databases, Factual
Microbial Sensitivity Tests
Staphylococcus aureus
Taiwan
Bacterial Proteins
Humans
Machine Learning
Anti-Bacterial Agents
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...
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...
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...
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