AIMC Topic: Ribosomes

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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...
Saccharomyces cerevisiae Ubiquitin Protein Interaction Mapping Saccharomyces cerevisiae Proteins Evolution, Molecular Models, Molecular Computer Simulation Protein Conformation Deep Learning Acyltransferases Protein Interaction Maps Homologous Recombination Computational Biology Chromosome Segregation Proteome Ligases Membrane Proteins DNA Repair Protein Biosynthesis Ribosomes Multiprotein Complexes
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Robotic end-to-end fusion of microtubules powered by kinesin.

Science robotics Nov 3, 2021
The active assembly of molecules by nanorobots has advanced greatly since “molecular manufacturing”—that is, the use of nanoscale tools to build molecular structures—was proposed. In contrast to a catalyst, which accelerates a reaction by smoothing t...
Escherichia coli Robotics Robotic Surgical Procedures Models, Biological Animals Biochemical Phenomena Drosophila melanogaster Rhodamines Kinesins Ribosomes Motion Adenosine Triphosphate Microtubules
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Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms.

Nature methods Oct 21, 2021
Cryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. However, automated identification of macromolecules inside cellular tomograms is challenged by noise and rec...
Macromolecular Substances Cryoelectron Microscopy Ribosomes Chlamydomonas reinhardtii Algorithms Deep Learning Image Processing, Computer-Assisted Electron Microscope Tomography Photosystem II Protein Complex Ribulose-Bisphosphate Carboxylase Neural Networks, Computer
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Predicting mean ribosome load for 5'UTR of any length using deep learning.

PLoS computational biology May 10, 2021
The 5' untranslated region plays a key role in regulating mRNA translation and consequently protein abundance. Therefore, accurate modeling of 5'UTR regulatory sequences shall provide insights into translational control mechanisms and help interpret ...
Humans Deep Learning RNA, Messenger Ribosomes 5' Untranslated Regions
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Full-length ribosome density prediction by a multi-input and multi-output model.

PLoS computational biology Mar 26, 2021
Translation elongation is regulated by a series of complicated mechanisms in both prokaryotes and eukaryotes. Although recent advance in ribosome profiling techniques has enabled one to capture the genome-wide ribosome footprints along transcripts at...
Peptide Chain Elongation, Translational Escherichia coli Saccharomyces cerevisiae Codon Ribosomes Computational Biology RNA, Messenger Models, Genetic Deep Learning
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LncLocation: Efficient Subcellular Location Prediction of Long Non-Coding RNA-Based Multi-Source Heterogeneous Feature Fusion.

International journal of molecular sciences Oct 1, 2020
Recent studies uncover that subcellular location of long non-coding RNAs (lncRNAs) can provide significant information on its function. Due to the lack of experimental data, the number of lncRNAs is very limited, experimentally verified subcellular l...
Humans Software Animals Computational Biology Gene Expression Regulation Benchmarking Base Sequence Exosomes Genome, Human Support Vector Machine Datasets as Topic Terminology as Topic Cytoplasm Databases, Genetic Cell Nucleus RNA, Long Noncoding Ribosomes Eukaryotic Cells
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Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping.

Nature communications Jul 15, 2020
Predicting effects of gene regulatory elements (GREs) is a longstanding challenge in biology. Machine learning may address this, but requires large datasets linking GREs to their quantitative function. However, experimental methods to generate such d...
Genome, Bacterial Ribosomes Regulatory Sequences, Nucleic Acid Datasets as Topic Phenotype Molecular Sequence Annotation Deep Learning Computational Biology Binding Sites Escherichia coli Gene Knockout Techniques Sequence Analysis, DNA High-Throughput Nucleotide Sequencing
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The hunt for sORFs: A multidisciplinary strategy.

Experimental cell research Mar 2, 2020
Growing evidence illustrates the shortcomings on the current understanding of the full complexity of the proteome. Previously overlooked small open reading frames (sORFs) and their encoded microproteins have filled important gaps, exerting their func...
Animals Computational Biology Ribosomes Humans Proteome High-Throughput Nucleotide Sequencing Neural Networks, Computer Plants Protein Biosynthesis Software Protein Sorting Signals Open Reading Frames
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NeuRiPP: Neural network identification of RiPP precursor peptides.

Scientific reports Sep 16, 2019
Significant progress has been made in the past few years on the computational identification of biosynthetic gene clusters (BGCs) that encode ribosomally synthesized and post-translationally modified peptides (RiPPs). This is done by identifying both...
Machine Learning Software Computational Biology Protein Processing, Post-Translational Humans Peptide Fragments Neural Networks, Computer Protein Biosynthesis Ribosomes
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Nervous-Like Circuits in the Ribosome Facts, Hypotheses and Perspectives.

International journal of molecular sciences Jun 14, 2019
In the past few decades, studies on translation have converged towards the metaphor of a "ribosome nanomachine"; they also revealed intriguing ribosome properties challenging this view. Many studies have shown that to perform an accurate protein synt...
Signal Transduction Humans Ribosomes Neural Networks, Computer Animals
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