RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation
Fig 4
Molecular dynamics simulations showing interactions of RBM5 and ELAVL1 with RNAs generated by RNAtranslator and Natural RNAs
(A) and (B) show simulation results for two RNA-binding proteins: RBM5 and ELAVL1, respectively. For each protein, three RNA sequences are compared: the RNA designed by RNAtranslator, a natural RNA known to bind the protein, and a randomly selected natural RNA. The top row displays free energy landscapes projected onto root-mean-square deviation (RMSD) and radius of gyration (RG). RNAtranslator achieves energy minima that are comparable to or deeper than those of natural binding RNAs. The bottom row presents simulation metrics over a 20-nanosecond trajectory. RNAtranslator forms more atomic contacts and achieves lower (i.e., more favorable) binding energies than random RNAs, and performs on par with or better than the natural binders. Hydrogen bonding distributions further support the binding of the predicted RNA-protein interactions.