AIMC Topic: Protein Biosynthesis

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Prioritization of genes for translation: a computational approach.

Expert review of proteomics Apr 9, 2024
INTRODUCTION: Gene identification for genetic diseases is critical for the development of new diagnostic approaches and personalized treatment options. Prioritization of gene translation is an important consideration in the molecular biology field, a...
Algorithms Precision Medicine Computational Biology Protein Biosynthesis Humans Machine Learning
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Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression.

Molecular systems biology Feb 14, 2024
Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in...
Polymorphism, Single Nucleotide RNA, Messenger Protein Biosynthesis Ribosomes Humans Machine Learning Catechol O-Methyltransferase
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Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides.

Nature communications Nov 8, 2023
Bioactive peptides are key molecules in health and medicine. Deep learning holds a big promise for the discovery and design of bioactive peptides. Yet, suitable experimental approaches are required to validate candidates in high throughput and at low...
DNA Replication Protein Biosynthesis Antimicrobial Peptides Deep Learning Molecular Dynamics Simulation
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DeepTESR: A Deep Learning Framework to Predict the Degree of Translational Elongation Short Ramp for Gene Expression Control.

ACS synthetic biology May 3, 2022
Controlling translational elongation is essential for efficient protein synthesis. Ribosome profiling has revealed that the speed of ribosome movement is correlated with translational efficiency in the translational elongation ramp. In this work, we ...
Deep Learning RNA, Messenger Escherichia coli Protein Biosynthesis Ribosomes Peptide Chain Elongation, Translational
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Inferring protein expression changes from mRNA in Alzheimer's dementia using deep neural networks.

Nature communications Feb 3, 2022
Identifying the molecular systems and proteins that modify the progression of Alzheimer's disease and related dementias (ADRD) is central to drug target selection. However, discordance between mRNA and protein abundance, and the scarcity of proteomic...
Female Aged Aged, 80 and over Male Humans Neural Networks, Computer Brain Dementia RNA-Seq RNA, Messenger Proteomics Transcriptome Deep Learning Cognitive Dysfunction Protein Biosynthesis Proteome Mass Spectrometry Alzheimer Disease
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Computed structures of core eukaryotic protein complexes.

Science (New York, N.Y.) Dec 10, 2021
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...
Protein Biosynthesis Ribosomes Multiprotein Complexes Chromosome Segregation Computer Simulation Ligases Deep Learning Acyltransferases Ubiquitin Protein Interaction Maps Homologous Recombination Membrane Proteins Computational Biology Protein Interaction Mapping Models, Molecular Saccharomyces cerevisiae Proteins Evolution, Molecular Proteome Protein Conformation DNA Repair Saccharomyces cerevisiae
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Protein Abundance Prediction Through Machine Learning Methods.

Journal of molecular biology Sep 23, 2021
Proteins are responsible for most physiological processes, and their abundance provides crucial information for systems biology research. However, absolute protein quantification, as determined by mass spectrometry, still has limitations in capturing...
Saccharomyces cerevisiae Proteins Protein Biosynthesis Schizosaccharomyces Kluyveromyces Codon Usage Enzymes Biological Evolution Algorithms Computational Biology Escherichia coli Saccharomyces cerevisiae Machine Learning
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Biomolecular simulation based machine learning models accurately predict sites of tolerability to the unnatural amino acid acridonylalanine.

Scientific reports Sep 15, 2021
The incorporation of unnatural amino acids (Uaas) has provided an avenue for novel chemistries to be explored in biological systems. However, the successful application of Uaas is often hampered by site-specific impacts on protein yield and solubilit...
Models, Molecular Amino Acids Molecular Conformation Protein Biosynthesis Machine Learning Proteins Structure-Activity Relationship
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A data-driven dimensionality-reduction algorithm for the exploration of patterns in biomedical data.

Nature biomedical engineering Nov 2, 2020
Dimensionality reduction is widely used in the visualization, compression, exploration and classification of data. Yet a generally applicable solution remains unavailable. Here, we report an accurate and broadly applicable data-driven algorithm for d...
Protein Biosynthesis Multifactor Dimensionality Reduction Humans Electroencephalography Algorithms Datasets as Topic Single-Cell Analysis Sequence Analysis, RNA Tomography, X-Ray Computed Biomedical Research
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The proteome landscape of the kingdoms of life.

Nature Jun 17, 2020
Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported, ...
Photosynthesis Proteome Ion Transport Bacteroides Animals Oxidation-Reduction Homeostasis Carbohydrate Metabolism Glycolysis Iron-Sulfur Proteins Peptides Proteolysis Chromatography Protein Folding Proteomics Deep Learning Protein Biosynthesis Classification Species Specificity
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