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

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 o...

Full description

Saved in:
Bibliographic Details
Published in:Journal of chemical information and modeling 2021-04, Vol.61 (4), p.1545-1549
Main Authors: Zhang, Kexin, Abdallah, Kyrillos, Ajmera, Pujan, Finos, Kyle, Looka, Andrew, Mekhael, Joseph, Frank, Aaron T
Format: Article
Language:English
Subjects:
Chemical equilibrium
Machine learning
NMR
Nuclear magnetic resonance
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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 ( S tructure-based MA chine L earning T ools for R NA) Science Gateway (smaltr.org).
ISSN:1549-9596
1549-960X
DOI:10.1021/acs.jcim.1c00006