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Basic workflow of DIRECT for RNA tertiary contact prediction. a The corresponding RNA multiple sequence alignment (MSA) is extracted from the Rfam database. The traditional direct-coupling analysis (DCA) predicts the tertiary contacts from sequence coevolution in MSA. b DIRECT then reweighs the contacts by using structural templates trained by Restricted Boltzmann Machine (RBM). c The reweighted contact prediction leads to better overall performance
