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Remote homology search with hidden Potts models

Fig 6

Gremlin-trained Potts models accurately predict 3D RNA contacts.

Top predicted 3D contacts from Gremlin-trained Potts models (cyan) against annotated nested base pairs (gray) and annotated tertiary contacts/pseudoknotted positions (pink) from the tRNA (A), Twister type P1 ribozyme (B), and SAM riboswitch (C) training alignments. For tRNA, annotated tertiary contacts are from a yeast tRNA-phe crystal structure [48]. A non-structural covariation between the tRNA discriminator base and the middle nucleotide in the anticodon (caused by aminoacyl-tRNA synthetase recognition preferences, not conserved base-pairing) is noted in orange [49].

doi: https://doi.org/10.1371/journal.pcbi.1008085.g006