DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach.

ABSTRACT: Designing RNA sequences that form a specific structure remains a challenge. Current computational methods often struggle with the complexity of RNA structures, especially when considering pseudoknots or restrictions related to RNA function. We developed DesiRNA, a computational tool for the design of RNA sequences based on the Replica Exchange Monte Carlo approach. It finds sequences that minimize a multiobjective scoring function, fulfill user-defined constraints and minimize the violation of restraints. DesiRNA handles pseudoknots, designs RNA-RNA complexes and sequences with alternative structures, prevents oligomerization of monomers, prevents folding into undesired structures and allows users to specify nucleotide composition preferences. In benchmarking tests, DesiRNA with a default

SUBMITTER: Wirecki TK 

PROVIDER: S-EPMC11744100 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature