AIMC Topic: RNA, Catalytic

Clear Filters Showing 1 to 4 of 4 articles

Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning.

Nature communications Aug 17, 2022
A neutral network connects all genotypes with equivalent phenotypes in a fitness landscape and plays an important role in the mutational robustness and evolvability of biomolecules. In contrast to earlier theoretical works, evidence of large neutral ...
Algorithms Deep Learning Genotype Models, Genetic Evolution, Molecular Mutation Genetic Fitness RNA, Catalytic
View on PubMed DOI

A convolutional neural network for the prediction and forward design of ribozyme-based gene-control elements.

eLife Apr 16, 2021
Ribozyme switches are a class of RNA-encoded genetic switch that support conditional regulation of gene expression across diverse organisms. An improved elucidation of the relationships between sequence, structure, and activity can improve our capaci...
Neural Networks, Computer Machine Learning Computer-Aided Design Aptamers, Nucleotide Sequence Analysis, RNA Models, Genetic Escherichia coli Structure-Activity Relationship Ligands High-Throughput Nucleotide Sequencing Gene Expression Regulation Base Sequence Nucleic Acid Conformation Saccharomyces cerevisiae RNA, Catalytic
View on PubMed DOI

gRNAde: A Geometric Deep Learning Pipeline for 3D RNA Inverse Design.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2025
Fundamental to the diverse biological functions of RNA are its 3D structure and conformational flexibility, which enable single sequences to adopt a variety of distinct 3D states. Currently, computational RNA design tasks are often posed as inverse p...
Neural Networks, Computer Software Deep Learning Computational Biology Models, Molecular RNA Nucleic Acid Conformation RNA, Catalytic
View on PubMed DOI

Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.

The Journal of chemical physics Dec 14, 2024
Molecular dynamics simulations are crucial for understanding the structural and dynamical behavior of biomolecular systems, including the impact of their environment. However, there is a gap between the time scale of these simulations and that of rea...
Deep Learning Magnesium Molecular Dynamics Simulation Nucleic Acid Conformation Monte Carlo Method RNA, Catalytic
View on PubMed DOI
Popular Topics
Recent Journals