AIMC Topic: Bacterial Proteins
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Deep protein representations enable recombinant protein expression prediction.
Computational biology and chemistry
Oct 27, 2021
A crucial process in the production of industrial enzymes is recombinant gene expression, which aims to induce enzyme overexpression of the genes in a host microbe. Current approaches for securing overexpression rely on molecular tools such as adjust...
Application of the random forest algorithm to Streptococcus pyogenes response regulator allele variation: from machine learning to evolutionary models.
Scientific reports
Jun 16, 2021
Group A Streptococcus (GAS) is a globally significant bacterial pathogen. The GAS genotyping gold standard characterises the nucleotide variation of emm, which encodes a surface-exposed protein that is recombinogenic and under immune-based selection ...
Evaluation of the VITEK 2 Advanced Expert System performance for predicting resistance mechanisms in Enterobacterales acquired from a hospital-based screening program.
Pathology
May 3, 2021
There is limited literature examining the accuracy of the VITEK 2 Advanced Expert System (AES) in characterisation of β-lactamase resistance patterns. We present a prospective single centre study to better ascertain the performance characteristics of...
Antibiofilm Activity of α-Amylase from Bacillus subtilis and Prediction of the Optimized Conditions for Biofilm Removal by Response Surface Methodology (RSM) and Artificial Neural Network (ANN).
Applied biochemistry and biotechnology
Mar 1, 2021
α-amylase is known to have antibiofilm activity against biofilms of both Gram positive and Gram-negative bacterial strains. Partially purified α-amylase from Bacillus subtilis was found to have inhibit biofilm formed by P. aeruginosa and S. aureus. T...
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...
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...
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...
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...
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....
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...
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