AIMC Topic: Protein Biosynthesis
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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...
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...
Dendritic trafficking faces physiologically critical speed-precision tradeoffs.
eLife
Dec 30, 2016
Nervous system function requires intracellular transport of channels, receptors, mRNAs, and other cargo throughout complex neuronal morphologies. Local signals such as synaptic input can regulate cargo trafficking, motivating the leading conceptual m...
Cell-Free Protein Synthesis as a Method to Rapidly Screen Machine Learning-Generated Protease Variants.
ACS synthetic biology
May 16, 2025
Machine learning (ML) tools have revolutionized protein structure prediction, engineering, and design, but the best ML tool is only as good as the training data it learns from. To obtain high-quality structural or functional data, protein purificatio...
Designer artificial environments for membrane protein synthesis.
Nature communications
May 10, 2025
Protein synthesis in natural cells involves intricate interactions between chemical environments, protein-protein interactions, and protein machinery. Replicating such interactions in artificial and cell-free environments can control the precision of...
Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis.
Circulation research
May 9, 2025
Angiogenesis, the formation of new blood vessels, is a fundamental biological process with implications for both physiological functions and pathological conditions. While the transcriptional regulation of angiogenesis, mediated by factors such as HI...
Analysis of RNA translation with a deep learning architecture provides new insight into translation control.
Nucleic acids research
Apr 10, 2025
Accurate annotation of coding regions in RNAs is essential for understanding gene translation. We developed a deep neural network to directly predict and analyze translation initiation and termination sites from RNA sequences. Trained with human tran...
[Research progress in mechanism models and artificial intelligence models for protein expression systems].
Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Mar 25, 2025
Proteins are the basic building blocks of life. Studying the protein expression mechanism is essential for understanding the cellular organization principles and the development of biotechnology. Protein expression, involving transcription, translati...
A deep learning model trained on expressed transcripts across different tissue types reveals cell-type codon-optimization preferences.
Nucleic acids research
Mar 20, 2025
Species-specific differences in protein translation can affect the design of protein-based drugs. Consequently, efficient expression of recombinant proteins often requires codon optimization. Publicly available optimization tools do not always result...
Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review.
Briefings in bioinformatics
Nov 22, 2024
Ribosome profiling (Ribo-seq) provides transcriptome-wide insights into protein synthesis dynamics, yet its analysis poses challenges, particularly for nonbioinformatics researchers. Large language model-based chatbots offer promising solutions by le...
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