Ribosomal engineering creates 'super-probiotic' bacteria with enhanced immune activation

Using ribosome engineering (RE), researchers from Shinshu University introduced mutations affecting the protein synthesis ...
GitHub

Evolutionary conservation of transcription factor binding sites

This repository contains the code, computing environment description, and software/package versions for the evolutionary conservation analysis of transcription factor binding sites based on Taipale ...
IEEE

A Deep Learning Framework for Protein-to-Metal Binding Prediction Using Protein Language Models

Abstract: This study presents an end-to-end deep learning framework for protein–to-metal-ion binding prediction, a critical task in understanding protein function, structural stability, and metal ...
eLife

Massively Parallel Polyribosome Profiling Reveals Translation Defects of Human Disease-Relevant UTR Mutations

The effort is timely and the paper carries valuable insights into the function of UTR mutations. There are still significant concerns about both the quality of the screen data, and its ability to ...
GitHub

UniSite: The First Cross-Structure Dataset and Learning Framework for End-to-End Ligand Binding Site Detection

The official implementation for "UniSite: The First Cross-Structure Dataset and Learning Framework for End-to-End Ligand Binding Site Detection". The detection of ligand binding sites for proteins is ...
C&EN

Construction of Promoter-Ribosome Binding Site Library for Manipulating Gene Expression in the Hyperthermophilic Archaeon Thermococcus kodakarensis

State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China ...
Frontiers

Iron responsive elements mRNA regulate Alzheimer’s amyloid precursor protein translation through iron sensing

Iron responsive element (IREs) mRNA and iron regulatory proteins (IRPs) regulate iron homeostasis. 5′-untranslated region motifs of APP IREs fold into RNA stem loops bind to IRP to control translation ...
Frontiers

Thermodynamic modeling of RsmA - mRNA interactions capture novel direct binding across the Pseudomonas aeruginosa transcriptome

Modeling interrogates all possible combinations of two binding sites across the provided sequence space and generates a measure of the ∆G mRNA:RsmA for each combination, per gene. These are then ...