RNA inverse folding using Monte Carlo tree search

Xiufeng Yang,Akito Taneda,Koji Tsuda,Kazuki Yoshizoe

doi:10.1186/s12859-017-1882-7

Xiufeng Yang, Akito Taneda + Show 2 more

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BackgroundArtificially synthesized RNA molecules provide important ways for creating a variety of novel functional molecules. State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of specific GC content, that fold into the target RNA structure. However, their performance is not satisfactory in complicated cases.ResultWe present a new inverse folding algorithm called MCTS-RNA, which uses Monte Carlo tree search (MCTS), a technique that has shown exceptional performance in Computer Go recently, to represent and discover the essential part of the sequence space. To obtain high accuracy, initial sequences generated by MCTS are further improved by a series of local updates. Our algorithm has an ability to control the GC content precisely and can deal with pseudoknot structures. Using common benchmark datasets for evaluation, MCTS-RNA showed a lot of promise as a standard method of RNA inverse folding.ConclusionMCTS-RNA is available at https://github.com/tsudalab/MCTS-RNA.

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Synthesized RNA molecules provide important ways for creating a variety of novel functional molecules
We develop a new algorithm called MCTSRNA that employs Monte Carlo tree search (MCTS) to solve the RNA inverse folding problem
Following [6], we used 29 Rfam families as target structures to evaluate the performance of MCTS-RNA for nested structures

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Synthesized RNA molecules provide important ways for creating a variety of novel functional molecules. State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of specific GC content, that fold into the target RNA structure. Their performance is not satisfactory in complicated cases. The function of RNA transcripts is tied to their three-dimensional molecular structures, itself primarily determined by secondary structures. For this reason, computational prediction of RNA secondary structure has been a popular subject of research for decades [1,2,3,4,5]. Dotu et al [8] performed RNA inverse folding of hammerhead ribozymes and experimentally validated the self-cleaving function of the designed ribozymes

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