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Databases, Protein

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Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach.

Database : the journal of biological databases and curation Jan 1, 2018
The precision medicine (PM) initiative promises to identify individualized treatment depending on a patients' genetic profile and their related responses. In order to help health professionals and researchers in the PM endeavor, BioCreative VI organi...
Databases, Protein Mutation Neural Networks, Computer Algorithms Protein Interaction Maps
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An end-to-end deep learning architecture for extracting protein-protein interactions affected by genetic mutations.

Database : the journal of biological databases and curation Jan 1, 2018
The BioCreative VI Track IV (mining protein interactions and mutations for precision medicine) challenge was organized in 2017 with the goal of applying biomedical text mining methods to support advancements in precision medicine approaches. As part ...
Neural Networks, Computer Databases, Protein Machine Learning Mutation Algorithms Protein Interaction Maps
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Hierarchical bi-directional attention-based RNNs for supporting document classification on protein-protein interactions affected by genetic mutations.

Database : the journal of biological databases and curation Jan 1, 2018
In this paper, we describe a hierarchical bi-directional attention-based Re-current Neural Network (RNN) as a reusable sequence encoder architecture, which is used as sentence and document encoder for document classification. The sequence encoder is ...
Neural Networks, Computer Algorithms Reproducibility of Results Databases, Protein Mutation Data Mining Protein Interaction Maps Models, Theoretical Support Vector Machine
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CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes.

BMC bioinformatics Dec 28, 2017
BACKGROUND: The β-Lactamase (BL) enzyme family is an important class of enzymes that plays a key role in bacterial resistance to antibiotics. As the newly identified number of BL enzymes is increasing daily, it is imperative to develop a computationa...
Algorithms beta-Lactamases Reproducibility of Results ROC Curve Databases, Protein Models, Molecular Amino Acid Sequence Neural Networks, Computer
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Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks.

Cell systems Dec 20, 2017
While genes are defined by sequence, in biological systems a protein's function is largely determined by its three-dimensional structure. Evolutionary information embedded within multiple sequence alignments provides a rich source of data for inferri...
Protein Conformation Protein Folding Sequence Alignment Models, Molecular Probability Forecasting Animals Computational Biology Proteins Databases, Protein Neural Networks, Computer Machine Learning Algorithms Humans
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Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

BMC bioinformatics Dec 6, 2017
BACKGROUND: Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has b...
Proteins Databases, Protein Amino Acids Software Computational Biology Models, Statistical Knowledge Bases Protein Interaction Mapping
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Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants.

Proteins Nov 29, 2017
Recent advances in computing power and machine learning empower functional annotation of protein sequences and their transcript variations. Here, we present an automated prediction system UniGOPred, for GO annotations and a database of GO term predic...
Humans Machine Learning Animals Sequence Analysis, Protein Models, Biological Transcriptome PTEN Phosphohydrolase Proteomics Gene Ontology Databases, Protein
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isGPT: An optimized model to identify sub-Golgi protein types using SVM and Random Forest based feature selection.

Artificial intelligence in medicine Nov 26, 2017
The Golgi Apparatus (GA) is a key organelle for protein synthesis within the eukaryotic cell. The main task of GA is to modify and sort proteins for transport throughout the cell. Proteins permeate through the GA on the ER (Endoplasmic Reticulum) fac...
Proteins Animals Amino Acid Sequence Humans Computational Biology Oligopeptides Databases, Protein Reproducibility of Results Support Vector Machine Golgi Apparatus
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pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning.

Analytical chemistry Nov 21, 2017
In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison between an experimental MS/MS spectrum and the theoretical spectra of the candidate peptides. Hence, accurate prediction of the theoretical spectra of peptides ap...
Proteome Databases, Protein Tandem Mass Spectrometry Deep Learning Proteomics Peptides
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Classification of G-protein coupled receptors based on a rich generation of convolutional neural network, N-gram transformation and multiple sequence alignments.

Amino acids Nov 18, 2017
Sequence classification is crucial in predicting the function of newly discovered sequences. In recent years, the prediction of the incremental large-scale and diversity of sequences has heavily relied on the involvement of machine-learning algorithm...
Algorithms Reproducibility of Results Models, Theoretical Sequence Alignment Neural Networks, Computer Databases, Protein Sequence Analysis, Protein Machine Learning Receptors, G-Protein-Coupled Amino Acid Sequence
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