AIMC Topic: Bacterial Proteins

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Revealing the inventory of type III effectors in Pantoea agglomerans gall-forming pathovars using draft genome sequences and a machine-learning approach.

Molecular plant pathology Feb 16, 2017
Pantoea agglomerans, a widespread epiphytic bacterium, has evolved into a hypersensitive response and pathogenicity (hrp)-dependent and host-specific gall-forming pathogen by the acquisition of a pathogenicity plasmid containing a type III secretion ...
DNA Mutational Analysis Pantoea Plant Tumors Machine Learning Bacterial Proteins Virulence
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Enhancing the Biological Relevance of Machine Learning Classifiers for Reverse Vaccinology.

International journal of molecular sciences Feb 1, 2017
Reverse vaccinology (RV) is a bioinformatics approach that can predict antigens with protective potential from the protein coding genomes of bacterial pathogens for subunit vaccine design. RV has become firmly established following the development of...
Bacterial Vaccines ROC Curve Humans Epitope Mapping Computational Biology Mutagenesis Machine Learning Vaccines, Subunit Support Vector Machine Area Under Curve Antigens, Bacterial Bacterial Proteins Epitopes
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Feature Fusion Based SVM Classifier for Protein Subcellular Localization Prediction.

Journal of integrative bioinformatics Dec 18, 2016
For the importance of protein subcellular localization in different branches of life science and drug discovery, researchers have focused their attentions on protein subcellular localization prediction. Effective representation of features from prote...
Models, Biological Support Vector Machine Bacterial Proteins Gram-Negative Bacteria
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ProClaT, a new bioinformatics tool for in silico protein reclassification: case study of DraB, a protein coded from the draTGB operon in Azospirillum brasilense.

BMC bioinformatics Dec 15, 2016
BACKGROUND: Azopirillum brasilense is a plant-growth promoting nitrogen-fixing bacteria that is used as bio-fertilizer in agriculture. Since nitrogen fixation has a high-energy demand, the reduction of N to NH by nitrogenase occurs only under limitin...
Operon Bacterial Proteins Computational Biology Genes, Bacterial Azospirillum brasilense Nitrogen Fixation Nitrogenase
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Improving protein-protein interactions prediction accuracy using protein evolutionary information and relevance vector machine model.

Protein science : a publication of the Protein Society Aug 9, 2016
Predicting protein-protein interactions (PPIs) is a challenging task and essential to construct the protein interaction networks, which is important for facilitating our understanding of the mechanisms of biological systems. Although a number of high...
Support Vector Machine Databases, Protein Bacterial Proteins Algorithms Protein Binding Saccharomyces cerevisiae Proteins Helicobacter pylori Saccharomyces cerevisiae
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Predicting pupylation sites in prokaryotic proteins using semi-supervised self-training support vector machine algorithm.

Analytical biochemistry May 16, 2016
As one important post-translational modification of prokaryotic proteins, pupylation plays a key role in regulating various biological processes. The accurate identification of pupylation sites is crucial for understanding the underlying mechanisms o...
Protein Processing, Post-Translational Bacterial Proteins Rhodococcus Algorithms Support Vector Machine Corynebacterium glutamicum
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Exploiting non-linear relationships between retention time and molecular structure of peptides originating from proteomes and comparing three multivariate approaches.

Journal of pharmaceutical and biomedical analysis Jan 27, 2016
Peptides' retention time prediction is gaining increasing popularity in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics. This is a promising approach for improving successful proteome mapping, useful both in identification ...
Models, Chemical Bacterial Proteins Tandem Mass Spectrometry HeLa Cells Quantitative Structure-Activity Relationship Protein Conformation Proteome Bacillus subtilis Chromatography, Liquid Artificial Intelligence Peptides Humans
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Prediction Enhancement of Residue Real-Value Relative Accessible Surface Area in Transmembrane Helical Proteins by Solving the Output Preference Problem of Machine Learning-Based Predictors.

Journal of chemical information and modeling Oct 20, 2015
The α-helical transmembrane proteins constitute 25% of the entire human proteome space and are difficult targets in high-resolution wet-lab structural studies, calling for accurate computational predictors. We present a novel sequence-based method ca...
Humans Machine Learning Animals Membrane Proteins Databases, Protein Models, Chemical Molecular Sequence Data Sequence Alignment Protein Structure, Quaternary Succinate Dehydrogenase Solubility Wolinella Bacterial Proteins Solvents Amino Acid Sequence Protein Structure, Secondary
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Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor.

BMC bioinformatics Sep 18, 2015
BACKGROUND: Two component systems (TCS) are signalling complexes manifested by a histidine kinase (receptor) and a response regulator (effector). They are the most abundant signalling pathways in prokaryotes and control a wide range of biological pro...
Protein Kinases Genome, Bacterial Histidine Kinase Area Under Curve Bacterial Proteins Protein Interaction Maps Bacteria ROC Curve Support Vector Machine
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Multi-location gram-positive and gram-negative bacterial protein subcellular localization using gene ontology and multi-label classifier ensemble.

BMC bioinformatics Aug 25, 2015
BACKGROUND: It has become a very important and full of challenge task to predict bacterial protein subcellular locations using computational methods. Although there exist a lot of prediction methods for bacterial proteins, the majority of these metho...
Gram-Negative Bacteria Gram-Positive Bacteria Protein Transport Bacterial Proteins Gene Ontology Intracellular Space
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