RNA Design: Methods and Protocols

by Alexander Churkin (Editor), Danny Barash (Editor)

Overview

This volume provides comprehensive methods on RNA design. Chapters details traditional RNA design in secondary structure, RNA design in tertiary structure, and RNA design applications and assessments. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory prools, and key tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, RNA Design: Methods and Prools aims to ensure successful results in the further study of this vital field.

Product Details

ISBN-13:	9781071640784
Publisher:	Springer US
Publication date:	10/25/2024
Series:	Methods in Molecular Biology , #2847
Edition description:	2025
Pages:	303
Product dimensions:	7.01(w) x 10.00(h) x (d)

Table of Contents

Sequence design for RNA-RNA interactions.- Sequence design using RNAStructure.- Riboswitch design using MODENA.- Complex in-silico RNA design with MoiRNAiFold.- Machine learning for RNA design – LEARNA.- Simulated Annealing for RNA design with SIMARD.- RNA design using incaRNAfbinv demonstrated with the identification of functional RNA motifs in hepatitis delta virus.- gRNAde: a geometric deep learning pipeline for 3D RNA inverse design.- Towards increasing the credibility of RNA design.- 3D-based RNA function prediction tools in rnaglib.- Generative modeling of RNA sequence families with restricted Boltzmann machines.- SHAPE probing to screen computationally designed RNA.- A computational approach for designing synthetic riboswitches for next-generation RNA therapeutics.- Monte Carlo inverse RNA folding.- Generating artificial ribozymes using sparse coevolutionary models.- Datasets for benchmarking RNA design algorithms.- The evolution of nucleic acid-based diagnosis methods from (pre-)CRISPR to CRISPR era and the associated machine/deep leaning approaches in relevant RNA design.