Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework.

ABSTRACT:

Motivation

The prediction of RNA structure canonical base pairs from a single sequence, especially pseudoknotted ones, remains challenging in a thermodynamic models that approximates the energy of the local 3D motifs joining canonical stems. It has become more and more apparent in recent years that the structural motifs in the loops, composed of noncanonical interactions, are essential for the final shape of the molecule enabling its multiple functions. Our capacity to predict accurate 3D structures is also limited when it comes to the organization of the large intricate network of interactions that form inside those loops.

Results

We previously developed the integer programming framework RNA Motifs over Integer Programming (RNAMoIP) to reconcile RNA secondary structure and

SUBMITTER: Loyer G 

PROVIDER: S-EPMC10868335 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature