AIMC Topic: Proteome

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DistilProtBert: a distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts.

Bioinformatics (Oxford, England) Sep 16, 2022
SUMMARY: Recently, deep learning models, initially developed in the field of natural language processing (NLP), were applied successfully to analyze protein sequences. A major drawback of these models is their size in terms of the number of parameter...
Amino Acid Sequence Sequence Analysis, Protein Natural Language Processing Amino Acids Humans Proteome
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Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling.

Bioinformatics (Oxford, England) Sep 15, 2022
MOTIVATION: Recent development of deep-learning methods has led to a breakthrough in the prediction accuracy of 3D protein structures. Extending these methods to protein pairs is expected to allow large-scale detection of protein-protein interactions...
Computational Biology Proteome Mitochondrial Proteins Humans Deep Learning
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DeepSCP: utilizing deep learning to boost single-cell proteome coverage.

Briefings in bioinformatics Jul 18, 2022
Multiplexed single-cell proteomes (SCPs) quantification by mass spectrometry greatly improves the SCP coverage. However, it still suffers from a low number of protein identifications and there is much room to boost proteins identification by computat...
Proteome Tandem Mass Spectrometry Deep Learning Proteomics Peptides
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Unbiased spatial proteomics with single-cell resolution in tissues.

Molecular cell Jun 16, 2022
Mass spectrometry (MS)-based proteomics has become a powerful technology to quantify the entire complement of proteins in cells or tissues. Here, we review challenges and recent advances in the LC-MS-based analysis of minute protein amounts, down to ...
Proteomics Proteome Artificial Intelligence Mass Spectrometry
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SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images.

Briefings in bioinformatics Mar 10, 2022
With the rapid growth of high-resolution microscopy imaging data, revealing the subcellular map of human proteins has become a central task in the spatial proteome. The cell atlas of the Human Protein Atlas (HPA) provides precious resources for recog...
Proteome Supervised Machine Learning Humans Neural Networks, Computer Fluorescent Antibody Technique
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DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning.

Briefings in bioinformatics Jan 17, 2022
Proteins with intrinsically disordered regions (IDRs) are common among eukaryotes. Many IDRs interact with nucleic acids and proteins. Annotation of these interactions is supported by computational predictors, but to date, only one tool that predicts...
DNA-Binding Proteins RNA Intrinsically Disordered Proteins Nucleic Acids Proteome DNA Computational Biology RNA-Binding Proteins Humans Deep Learning Protein Binding Neural Networks, Computer
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Enhancing the Discovery of Functional Post-Translational Modification Sites with Machine Learning Models - Development, Validation, and Interpretation.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Protein posttranslational modifications (PTMs) are a rapidly expanding feature class of significant importance in cell biology. Due to a high burden of experimental proof, the number of functionals PTMs in the eukaryotic proteome is currently underes...
Protein Processing, Post-Translational Machine Learning Neural Networks, Computer Proteome
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Predicting Proteome-Scale Protein Structure with Artificial Intelligence.

The New England journal of medicine Dec 2, 2021
Computer Simulation Computational Biology Proteome Databases, Protein Humans Artificial Intelligence Protein Conformation
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Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.

Briefings in bioinformatics Sep 2, 2021
This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusabl...
International Cooperation Self-Assessment Proteome Metadata Humans Data Management Plants Workflow Genome, Human Neural Networks, Computer Proteomics High-Throughput Nucleotide Sequencing Software Phenotype
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Protein subcellular localization based on deep image features and criterion learning strategy.

Briefings in bioinformatics Jul 20, 2021
The spatial distribution of proteome at subcellular levels provides clues for protein functions, thus is important to human biology and medicine. Imaging-based methods are one of the most important approaches for predicting protein subcellular locati...
Image Processing, Computer-Assisted Humans Neural Networks, Computer Proteome
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