AIMC Topic: Protein Interaction Mapping

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Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

Scientific reports Jun 16, 2017
The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are impo...
Humans Protein Interaction Mapping Protein Disulfide-Isomerases Protein Interaction Domains and Motifs Oxidation-Reduction Machine Learning Molecular Dynamics Simulation Protein Interaction Maps Protein Conformation
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NewGOA: Predicting New GO Annotations of Proteins by Bi-Random Walks on a Hybrid Graph.

IEEE/ACM transactions on computational biology and bioinformatics Jun 15, 2017
A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many ...
Humans Protein Interaction Maps Computational Biology Protein Interaction Mapping Saccharomyces cerevisiae Proteins Proteins Molecular Sequence Annotation Gene Ontology
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Machine learning based identification of protein-protein interactions using derived features of physiochemical properties and evolutionary profiles.

Artificial intelligence in medicine Jun 13, 2017
Proteins are the central constitute of a cell or biological system. Proteins execute their functions by interacting with other molecules such as RNA, DNA and other proteins. The major functionality of protein-protein interactions (PPIs) is the execut...
Algorithms Computational Biology Support Vector Machine Proteins Protein Interaction Mapping Machine Learning
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Editorial-Sequences and topology.

Current opinion in structural biology Jun 4, 2017
Humans Computational Biology Protein Interaction Domains and Motifs Machine Learning Thermodynamics Molecular Docking Simulation Proteins Protein Conformation, alpha-Helical Animals Protein Interaction Mapping Binding Sites Protein Conformation, beta-Strand Protein Multimerization Protein Binding
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DeepPPI: Boosting Prediction of Protein-Protein Interactions with Deep Neural Networks.

Journal of chemical information and modeling May 26, 2017
The complex language of eukaryotic gene expression remains incompletely understood. Despite the importance suggested by many proteins variants statistically associated with human disease, nearly all such variants have unknown mechanisms, for example,...
Saccharomyces cerevisiae Protein Interaction Mapping Neural Networks, Computer
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InterPred: A pipeline to identify and model protein-protein interactions.

Proteins Mar 21, 2017
Protein-protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time-consuming. The fact that the numb...
Sequence Analysis, Protein Protein Interaction Domains and Motifs Amino Acid Sequence Protein Interaction Mapping Molecular Docking Simulation Computational Biology Support Vector Machine Proteins Internet Software Benchmarking
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Prior knowledge guided active modules identification: an integrated multi-objective approach.

BMC systems biology Mar 14, 2017
BACKGROUND: Active module, defined as an area in biological network that shows striking changes in molecular activity or phenotypic signatures, is important to reveal dynamic and process-specific information that is correlated with cellular or diseas...
Machine Learning Saccharomyces cerevisiae Gene Regulatory Networks Protein Interaction Mapping Computational Biology Galactose
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Imputation for transcription factor binding predictions based on deep learning.

PLoS computational biology Feb 24, 2017
Understanding the cell-specific binding patterns of transcription factors (TFs) is fundamental to studying gene regulatory networks in biological systems, for which ChIP-seq not only provides valuable data but is also considered as the gold standard....
Humans Neural Networks, Computer Transcription Factors Machine Learning Hep G2 Cells High-Throughput Nucleotide Sequencing Protein Interaction Mapping Reproducibility of Results K562 Cells Chromatin Immunoprecipitation Sensitivity and Specificity Binding Sites Protein Binding
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Evaluating the effect of annotation size on measures of semantic similarity.

Journal of biomedical semantics Feb 13, 2017
BACKGROUND: Ontologies are widely used as metadata in biological and biomedical datasets. Measures of semantic similarity utilize ontologies to determine how similar two entities annotated with classes from ontologies are, and semantic similarity is ...
Disease Molecular Sequence Annotation Gene Ontology Protein Interaction Mapping Semantics
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Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.

PloS one Jan 24, 2017
Protein-protein docking protocols aim to predict the structures of protein-protein complexes based on the structure of individual partners. Docking protocols usually include several steps of sampling, clustering, refinement and re-scoring. The scorin...
Models, Molecular Monte Carlo Method Models, Chemical Computer Simulation Knowledge Bases Molecular Docking Simulation Protein Interaction Mapping Linear Models Software Protein Binding Protein Conformation Algorithms
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