CS-Annotate: A Tool for Using NMR Chemical Shifts to Annotate RNA Structure

Abstract

Here, we introduce CS-Annotate, a tool that uses assigned NMR chemical shifts to annotate structural features in RNA. At its core, CS-Annotate is a deployment of a multitask deep learning model that simultaneously classifies the solvent exposure, base-stacking and-pairing status, and conformation of individual RNA residues from their chemical shift fingerprint. Here, we briefly describe how we trained and tested the classifier and demonstrate its application to a model RNA system. CS-Annotate can be accessed via the SMALTR (Structure-based MAchine Learning Tools for RNA) Science Gateway (smaltr.org).