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It is acknowledged that co-evolutionary nucleotide-nucleotide interactionsare essential for RNA structures and functions. Currently, direct couplinganalysis (DCA) infers nucleotide contacts in a sequence from its homologoussequence alignment across different species. DCA and similar approaches thatuse sequence information alone usually yield a low accuracy, especially whenthe available homologous sequences are limited. Here we present a new methodthat incorporates a Restricted Boltzmann Machine (RBM) to augment theinformation on sequence co-variations with structural patterns in contactinference. We thus name our method DIRECT that stands for Direct InformationREweighted by Contact Templates. Benchmark tests demonstrate that DIRECTproduces a substantial enhancement of 13% in accuracy on average for contactprediction in comparison to the traditional DCA. These results suggest thatDIRECT could be used for improving predictions of RNA tertiary structures andfunctions. The source codes and dataset of DIRECT are available at http://http://zhao.phy.ccnu.edu.cn:8122/DIRECT/index.html.

Direct Information Reweighted by Contact Templates: Improved RNA Contact Prediction by Combining Structural Features