RCPred: RNA complex prediction as a constrained maximum weight clique problem.

ABSTRACT:

Background

RNAs can interact and form complexes, which have various biological roles. The secondary structure prediction of those complexes is a first step towards the identification of their 3D structure. We propose an original approach that takes advantage of the high number of RNA secondary structure and RNA-RNA interaction prediction tools. We formulate the problem of RNA complex prediction as the determination of the best combination (according to the free energy) of predicted RNA secondary structures and RNA-RNA interactions.

Results

We model those predicted structures and interactions as a graph in order to have a combinatorial optimization problem that is a constrained maximum weight clique problem. We propose an heuristic based on Breakout Local Search to solve this

SUBMITTER: Legendre A 

PROVIDER: S-EPMC6439972 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature