LinearDesign is out! (from the authors of LinearFold and LinearPartition)

Gameplay and Strategies Tools
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It turns out we can computationally design the most stable mRNA sequence for any given protein. For the spike protein of SARS-CoV-2 (which Moderna uses for its mRNA-1273 vaccine), LinearDesign exact mode takes ~1.6 hours (achieving free energy -2477.7 kcal/mol), and LinearDesign beam size b=1000 takes ~20 minutes with ~0.6% free energy loss.

By comparison, the wild type (in the virus) is only -1075.4 kcal/mol, and the best random sequence (among 5,000 sequences taken randomly but using codons proportional to human codon usage) is -1220.3 kcal/mol, suggesting that the designed mRNA sequence is far more stable.

paper: https://arxiv.org/abs/2004.10177
webserver: http://rna.baidu.com/

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It would be interesting to compare the WT virus mRNA to the LinearDesign stabilized mRNA to see what mutations were used and where they were applied. We could do a lot with that information. 
Congratulations on this achievement!  

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LinearDesign-3 was chosen for the first round of Spike designs being tested, which is Round 3 of the OpenVaccine Project.

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Thanks again Omei!

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