AIMC Topic: Bacterial Proteins

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QSSR Modeling of Bacillus Subtilis Lipase A Peptide Collision Cross-Sections in Ion Mobility Spectrometry: Local Descriptor Versus Global Descriptor.

The protein journal Jan 16, 2021
To investigate the structure-dependent peptide mobility behavior in ion mobility spectrometry (IMS), quantitative structure-spectrum relationship (QSSR) is systematically modeled and predicted for the collision cross section Ω values of totally 162 s...
Bacillus subtilis Principal Component Analysis Least-Squares Analysis Support Vector Machine Lipase Quantitative Structure-Activity Relationship Monte Carlo Method Ion Mobility Spectrometry Bacterial Proteins Amino Acids Oligopeptides
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Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome.

Nature communications Dec 11, 2020
The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcrip...
Iron Chelating Agents Ethanol DNA Damage Histidine Bacterial Proteins Transcriptome Gene Regulatory Networks Machine Learning Bacillus subtilis Quorum Sensing Data Mining Gene Expression Regulation, Bacterial Tryptophan
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Machine learning-based prediction of enzyme substrate scope: Application to bacterial nitrilases.

Proteins Nov 10, 2020
Predicting the range of substrates accepted by an enzyme from its amino acid sequence is challenging. Although sequence- and structure-based annotation approaches are often accurate for predicting broad categories of substrate specificity, they gener...
Bacterial Proteins Ligands Chemical Phenomena Catalytic Domain Machine Learning Molecular Docking Simulation Protein Binding Nitriles Aminohydrolases
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Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches.

Scientific reports Oct 22, 2020
Rifampicin resistance is a major therapeutic challenge, particularly in tuberculosis, leprosy, P. aeruginosa and S. aureus infections, where it develops via missense mutations in gene rpoB. Previously we have highlighted that these mutations reduce p...
Mutation, Missense Leprosy Mycobacterium leprae Staphylococcal Infections Mycobacterium tuberculosis Rifampin Machine Learning Drug Resistance, Bacterial Staphylococcus aureus Bacterial Proteins Antitubercular Agents Tuberculosis Humans
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Predicting Gram-Positive Bacterial Protein Subcellular Location by Using Combined Features.

BioMed research international Aug 2, 2020
There are a lot of bacteria in the environment, and Gram-positive bacteria are the most common ones. Some Gram-positive bacteria are very harmful to the human body, so it is significant to predict Gram-positive bacterial protein subcellular location....
Databases, Protein Humans Gram-Positive Bacteria Bacterial Proteins Computational Biology Models, Biological Support Vector Machine
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Signal Peptides Generated by Attention-Based Neural Networks.

ACS synthetic biology Jul 27, 2020
Short (15-30 residue) chains of amino acids at the amino termini of expressed proteins known as signal peptides (SPs) specify secretion in living cells. We trained an attention-based neural network, the Transformer model, on data from all available o...
Bacterial Proteins Protein Sorting Signals Bacillus subtilis Databases, Protein Area Under Curve Machine Learning ROC Curve
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Use of Chou's 5-steps rule to predict the subcellular localization of gram-negative and gram-positive bacterial proteins by multi-label learning based on gene ontology annotation and profile alignment.

Journal of integrative bioinformatics Jun 29, 2020
To date, many proteins generated by large-scale genome sequencing projects are still uncharacterized and subject to intensive investigations by both experimental and computational means. Knowledge of protein subcellular localization (SCL) is of key i...
Machine Learning Molecular Sequence Annotation Gene Ontology Sequence Alignment Sequence Analysis, Protein Subcellular Fractions Gene Expression Profiling Computational Biology Databases, Protein Bacterial Proteins Gram-Negative Bacteria Gram-Positive Bacteria
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Photosynthetic protein classification using genome neighborhood-based machine learning feature.

Scientific reports Apr 28, 2020
Identification of novel photosynthetic proteins is important for understanding and improving photosynthetic efficiency. Synergistically, genome neighborhood can provide additional useful information to identify photosynthetic proteins. We, therefore,...
Bacteria Models, Genetic Support Vector Machine Photosynthesis Bacterial Proteins Genome, Bacterial
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ACNNT3: Attention-CNN Framework for Prediction of Sequence-Based Bacterial Type III Secreted Effectors.

Computational and mathematical methods in medicine Apr 3, 2020
The type III secretion system (T3SS) is a special protein delivery system in Gram-negative bacteria which delivers T3SS-secreted effectors (T3SEs) to host cells causing pathological changes. Numerous experiments have verified that T3SEs play importan...
Type III Secretion Systems Neural Networks, Computer Computational Biology Deep Learning Amino Acid Sequence Databases, Protein Bacterial Proteins Gram-Negative Bacteria Host Microbial Interactions
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Artificial Intelligence and Machine learning based prediction of resistant and susceptible mutations in Mycobacterium tuberculosis.

Scientific reports Mar 26, 2020
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis (M.tb), causes highest number of deaths globally for any bacterial disease necessitating novel diagnosis and treatment strategies. High-throughput sequencing methods genera...
Mycobacterium tuberculosis Genes, Bacterial Genes, MDR Humans Mutation Artificial Intelligence Tuberculosis, Multidrug-Resistant Molecular Dynamics Simulation Drug Resistance, Multiple, Bacterial Machine Learning Polymorphism, Single Nucleotide Bayes Theorem Algorithms Bacterial Proteins Molecular Docking Simulation
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