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

TL;DR

This paper introduces DIRECT, a novel method combining co-evolutionary analysis with structural contact templates using RBM, significantly improving RNA contact prediction accuracy over traditional DCA methods.

Contribution

The paper presents a new approach that integrates structural contact templates with co-evolutionary data using RBM, enhancing RNA contact prediction accuracy.

Findings

13% average accuracy improvement over DCA

Effective in predicting RNA tertiary structures

Open-source implementation available

Abstract

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