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Gram-Positive Bacteria

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Designing antimicrobial peptides using deep learning and molecular dynamic simulations.

Briefings in bioinformatics Mar 19, 2023
With the emergence of multidrug-resistant bacteria, antimicrobial peptides (AMPs) offer promising options for replacing traditional antibiotics to treat bacterial infections, but discovering and designing AMPs using traditional methods is a time-cons...
Anti-Bacterial Agents Antimicrobial Cationic Peptides Gram-Negative Bacteria Molecular Dynamics Simulation Gram-Positive Bacteria Deep Learning Antimicrobial Peptides
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Deep-ABPpred: identifying antibacterial peptides in protein sequences using bidirectional LSTM with word2vec.

Briefings in bioinformatics Sep 2, 2021
The overuse of antibiotics has led to emergence of antimicrobial resistance, and as a result, antibacterial peptides (ABPs) are receiving significant attention as an alternative. Identification of effective ABPs in lab from natural sources is a cost-...
Viral Tail Proteins Drug Resistance, Bacterial Peptides Streptococcus Phages Gram-Negative Bacteria Gram-Positive Bacteria Computational Biology Amino Acid Sequence Anti-Bacterial Agents Deep Learning
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DeeplyEssential: a deep neural network for predicting essential genes in microbes.

BMC bioinformatics Sep 30, 2020
BACKGROUND: Essential genes are those genes that are critical for the survival of an organism. The prediction of essential genes in bacteria can provide targets for the design of novel antibiotic compounds or antimicrobial strategies.
Bacteria Cluster Analysis Genes, Essential Neural Networks, Computer ROC Curve Gram-Positive Bacteria Area Under Curve Codon Gram-Negative Bacteria
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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...
Gene Ontology Sequence Alignment Sequence Analysis, Protein Gram-Positive Bacteria Molecular Sequence Annotation Subcellular Fractions Gene Expression Profiling Computational Biology Bacterial Proteins Gram-Negative Bacteria Databases, Protein Machine Learning
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Fast Pathogen Identification Using Single-Cell Matrix-Assisted Laser Desorption/Ionization-Aerosol Time-of-Flight Mass Spectrometry Data and Deep Learning Methods.

Analytical chemistry Jun 2, 2020
In diagnostics of infectious diseases, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) can be applied for the identification of pathogenic microorganisms. However, to achieve a trustworthy identification fr...
Gram-Positive Bacteria Aerosols Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Gram-Negative Bacteria Deep Learning Single-Cell Analysis
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Predicting Gram-Positive Bacterial Protein Subcellular Location by Using Combined Features.

BioMed research international Jan 1, 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....
Bacterial Proteins Humans Models, Biological Computational Biology Support Vector Machine Gram-Positive Bacteria Databases, Protein
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Distribution of main Gram-positive pathogens causing bloodstream infections in United States and European hospitals during the SENTRY Antimicrobial Surveillance Program (2010-2016): concomitant analysis of oritavancin in vitro activity.

Journal of chemotherapy (Florence, Italy) Sep 1, 2018
This study updates the distribution and trends of Gram-positive organisms causing bloodstream infections (BSIs) in the United States (US) and Europe during 2010-2016. In vitro activities of oritavancin and comparators were also evaluated. Staphylococ...
Hospitals Europe Humans Gram-Positive Bacterial Infections Bacteremia Anti-Bacterial Agents Cross Infection Gram-Positive Bacteria Lipoglycopeptides United States
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EvoStruct-Sub: An accurate Gram-positive protein subcellular localization predictor using evolutionary and structural features.

Journal of theoretical biology Apr 14, 2018
Determining subcellular localization of proteins is considered as an important step towards understanding their functions. Previous studies have mainly focused solely on Gene Ontology (GO) as the main feature to tackle this problem. However, it was s...
Computational Biology Databases, Protein Bacterial Proteins Support Vector Machine Gram-Positive Bacteria Gene Ontology
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Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming.

IEEE/ACM transactions on computational biology and bioinformatics Jan 1, 2017
Growing bacterial resistance to antibiotics is spurring research on utilizing naturally-occurring antimicrobial peptides (AMPs) as templates for novel drug design. While experimentalists mainly focus on systematic point mutations to measure the effec...
Genetic Engineering Machine Learning Algorithms Neural Networks, Computer Drug Design Computational Biology Antimicrobial Cationic Peptides Gram-Negative Bacteria Decision Trees Gram-Positive Bacteria
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Predict Gram-Positive and Gram-Negative Subcellular Localization via Incorporating Evolutionary Information and Physicochemical Features Into Chou's General PseAAC.

IEEE transactions on nanobioscience Dec 1, 2015
In this study, we used structural and evolutionary based features to represent the sequences of gram-positive and gram-negative subcellular localizations. To do this, we proposed a normalization method to construct a normalize Position Specific Scori...
Bayes Theorem Gram-Negative Bacteria Gram-Positive Bacteria Support Vector Machine Intracellular Space Models, Statistical
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