AIMC Topic: Bacterial Proteins

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Machine learning predicts new anti-CRISPR proteins.

Nucleic acids research May 21, 2020
The increasing use of CRISPR-Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR-Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that...
Machine Learning Sequence Analysis, Protein CRISPR-Associated Protein 9 Prophages Proteome Bacterial Proteins Streptococcus
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Recent Advancement in Predicting Subcellular Localization of Mycobacterial Protein with Machine Learning Methods.

Medicinal chemistry (Shariqah (United Arab Emirates)) Jan 1, 2020
Mycobacterium tuberculosis (MTB) can cause the terrible tuberculosis (TB), which is reported as one of the most dreadful epidemics. Although many biochemical molecular drugs have been developed to cope with this disease, the drug resistance-especiall...
Bacterial Proteins Mycobacterium tuberculosis Machine Learning Computational Biology
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DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence.

Bioinformatics (Oxford, England) Jun 1, 2019
MOTIVATION: Various bacterial pathogens can deliver their secreted substrates also called effectors through Type III secretion systems (T3SSs) into host cells and cause diseases. Since T3SS secreted effectors (T3SEs) play important roles in pathogen-...
Neural Networks, Computer Bacterial Proteins Gram-Negative Bacteria Genome, Bacterial Software Algorithms
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Bastion3: a two-layer ensemble predictor of type III secreted effectors.

Bioinformatics (Oxford, England) Jun 1, 2019
MOTIVATION: Type III secreted effectors (T3SEs) can be injected into host cell cytoplasm via type III secretion systems (T3SSs) to modulate interactions between Gram-negative bacterial pathogens and their hosts. Due to their relevance in pathogen-hos...
Machine Learning Gram-Negative Bacteria Computational Biology Software Bacterial Proteins Algorithms Amino Acid Sequence
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Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.

Briefings in bioinformatics May 21, 2019
In the course of infecting their hosts, pathogenic bacteria secrete numerous effectors, namely, bacterial proteins that pervert host cell biology. Many Gram-negative bacteria, including context-dependent human pathogens, use a type IV secretion syste...
Machine Learning Bacterial Proteins Bacterial Secretion Systems Algorithms Support Vector Machine Bayes Theorem
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An account of in silico identification tools of secreted effector proteins in bacteria and future challenges.

Briefings in bioinformatics Jan 18, 2019
Bacterial pathogens secrete numerous effector proteins via six secretion systems, type I to type VI secretion systems, to adapt to new environments or to promote virulence by bacterium-host interactions. Many computational approaches have been used i...
Bacterial Secretion Systems Host Microbial Interactions Models, Biological Virulence Markov Chains Databases, Factual Computer Simulation Computational Biology Support Vector Machine Bayes Theorem Bacterial Proteins Neural Networks, Computer Machine Learning Algorithms Humans
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Prediction of human-Bacillus anthracis protein-protein interactions using multi-layer neural network.

Bioinformatics (Oxford, England) Dec 15, 2018
MOTIVATION: Triplet amino acids have successfully been included in feature selection to predict human-HPV protein-protein interactions (PPI). The utility of supervised learning methods is curtailed due to experimental data not being available in suff...
Bacillus anthracis Computational Biology Support Vector Machine Proteins Humans Models, Molecular Neural Networks, Computer Bacterial Proteins Protein Interaction Mapping
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CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction.

Bioinformatics (Oxford, England) Aug 1, 2018
MOTIVATION: Coenzyme A (CoA)-protein binding plays an important role in various cellular functions and metabolic pathways. However, no computational methods can be employed for CoA-binding residues prediction.
Computational Biology Support Vector Machine Proteins Models, Molecular Bacterial Proteins Protein Conformation Software Protein Binding Coenzyme A Sequence Analysis, Protein Vibrio cholerae Acetyltransferases
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Enhancing fluorescent protein photostability through robot-assisted photobleaching.

Integrative biology : quantitative biosciences from nano to macro Jul 16, 2018
Improving fluorescent proteins through the use of directed evolution requires robust techniques for screening large libraries of genetic variants. Here we describe an effective and relatively low-cost system for screening libraries of fluorescent pro...
Photochemistry Escherichia coli Robotics Luminescent Proteins HeLa Cells Humans Mutation Bacterial Proteins Photobleaching Plasmids Models, Biological Crystallography, X-Ray Light
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The influence of vitamin D deficiency on eradication rates of Helicobacter pylori.

Advances in clinical and experimental medicine : official organ Wroclaw Medical University Dec 1, 2017
BACKGROUND: Helicobacter pylori eradication therapy improves the healing of various gastro-duodenal diseases such as chronic gastritis and peptic ulcer, and also reduces gastric cancer incidence. Several studies have reported on risk factors other th...
Antigens, Bacterial Middle Aged Aged Humans Adult Vitamin D Bacterial Proteins Female Male Vitamin D Deficiency Helicobacter Infections Helicobacter pylori
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