RNA design via structure-aware multifrontier ensemble optimization.

ABSTRACT:

Motivation

RNA design is the search for a sequence or set of sequences that will fold to desired structure, also known as the inverse problem of RNA folding. However, the sequences designed by existing algorithms often suffer from low ensemble stability, which worsens for long sequence design. Additionally, for many methods only a small number of sequences satisfying the MFE criterion can be found by each run of design. These drawbacks limit their use cases.

Results

We propose an innovative optimization paradigm, SAMFEO, which optimizes ensemble objectives (equilibrium probability or ensemble defect) by iterative search and yields a very large number of successfully designed RNA sequences as byproducts. We develop a search method which leverages structure level and ensemble

SUBMITTER: Zhou T 

PROVIDER: S-EPMC10311297 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature