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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...
Algorithms Bacterial Proteins Helicobacter pylori Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins Protein Binding Support Vector Machine Databases, Protein
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In Silico Prediction of Gamma-Aminobutyric Acid Type-A Receptors Using Novel Machine-Learning-Based SVM and GBDT Approaches.

BioMed research international Aug 8, 2016
Gamma-aminobutyric acid type-A receptors (GABAARs) belong to multisubunit membrane spanning ligand-gated ion channels (LGICs) which act as the principal mediators of rapid inhibitory synaptic transmission in the human brain. Therefore, the category p...
Algorithms Humans Ligands Support Vector Machine Machine Learning Brain Receptors, GABA-A Computer Simulation Amino Acid Motifs Decision Making Reproducibility of Results Decision Trees Models, Statistical Computational Biology Databases, Protein Amino Acids
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Positive-Unlabeled Learning for Pupylation Sites Prediction.

BioMed research international Aug 7, 2016
Pupylation plays a key role in regulating various protein functions as a crucial posttranslational modification of prokaryotes. In order to understand the molecular mechanism of pupylation, it is important to identify pupylation substrates and sites ...
Lysine Binding Sites Ubiquitination Protein Processing, Post-Translational Machine Learning Proteins Algorithms Databases, Protein Support Vector Machine
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Revealing disease-associated pathways by network integration of untargeted metabolomics.

Nature methods Aug 1, 2016
Uncovering the molecular context of dysregulated metabolites is crucial to understand pathogenic pathways. However, their system-level analysis has been limited owing to challenges in global metabolite identification. Most metabolite features detecte...
Sphingolipids Huntington Disease Databases, Protein Metabolic Networks and Pathways Fatty Acids Humans Steroids Neural Networks, Computer Metabolomics Machine Learning Algorithms
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A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.

International journal of molecular sciences Jul 27, 2016
Understanding protein-protein interactions is a key challenge in biochemistry. In this work, we describe a more accurate methodology to predict Hot-Spots (HS) in protein-protein interfaces from their native complex structure compared to previous publ...
Protein Interaction Mapping Protein Interaction Domains and Motifs Humans Machine Learning Algorithms Databases, Protein Computational Biology Protein Conformation Proteins
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Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.

Journal of proteome research Jul 22, 2016
A central problem in mass spectrometry analysis involves identifying, for each observed tandem mass spectrum, the corresponding generating peptide. We present a dynamic Bayesian network (DBN) toolkit that addresses this problem by using a machine lea...
Peptides Proteomics Databases, Protein Machine Learning Software Bayes Theorem Tandem Mass Spectrometry
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Machine Learning of Protein Interactions in Fungal Secretory Pathways.

PloS one Jul 21, 2016
In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict prote...
Fungal Proteins Saccharomyces cerevisiae Trichoderma Secretory Pathway Protein Interaction Mapping Genome, Fungal Machine Learning Evolution, Molecular Databases, Protein Amino Acid Sequence Algorithms ROC Curve Protein Interaction Maps
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An improved method for predicting interactions between virus and human proteins.

Journal of bioinformatics and computational biology Jul 10, 2016
The interaction of virus proteins with host proteins plays a key role in viral infection and consequent pathogenesis. Many computational methods have been proposed to predict protein-protein interactions (PPIs), but most of the computational methods ...
Alphapapillomavirus Databases, Protein Amino Acids Reproducibility of Results Hepacivirus Computational Biology Viral Proteins Support Vector Machine Humans Protein Interaction Mapping Host-Pathogen Interactions Gene Ontology
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The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.

Database : the journal of biological databases and curation Jul 3, 2016
Genomics, epigenomics, transcriptomics, proteomics and metabolomics efforts rapidly generate a plethora of data on the activity and levels of biomolecules within mammalian cells. At the same time, curation projects that organize knowledge from the bi...
Humans Databases, Protein Data Mining Machine Learning Databases, Nucleic Acid Animals Mice
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gDNA-Prot: Predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of protein sequence.

Journal of theoretical biology Jul 1, 2016
DNA-binding proteins are the functional proteins in cells, which play an important role in various essential biological activities. An effective and fast computational method gDNA-Prot is proposed to predict DNA-binding proteins in this paper, which ...
Computational Biology Support Vector Machine Databases, Protein Principal Component Analysis ROC Curve Numerical Analysis, Computer-Assisted DNA-Binding Proteins Amino Acid Sequence Genome DNA Models, Molecular Protein Domains
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