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Bioinformatics. 2019 Aug 2. pii: btz611. doi: 10.1093/bioinformatics/btz611. [Epub ahead of print]

RAG-Web: RNA Structure Prediction/Design using RNA-As-Graphs.

Author information

1
Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East, New York, NY, USA.
2
Department of Chemistry, Smith College, Northampton, MA, USA.
3
Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY, USA.
4
NYU-ECNU Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, North Zhongshan Road, Shanghai, China.

Abstract

MOTIVATION:

We launch a webserver for RNA structure prediction and design corresponding to tools developed using our RNA-As-Graphs (RAG) approach. RAG uses coarse-grained tree graphs to represent RNA secondary structure, allowing the application of graph theory to analyze and advance RNA structure discovery. Our webserver consists of three modules: (a) RAG Sampler: samples tree graph topologies from an RNA secondary structure to predict corresponding tertiary topologies, (b) RAG Builder: builds three-dimensional atomic models from candidate graphs generated by RAG Sampler, and (c) RAG Designer: designs sequences that fold onto novel RNA motifs (described by tree graph topologies). Results analyses are performed for further assessment/selection. The Results page provides links to download results and indicates possible errors encountered. RAG-Web offers a user-friendly interface to utilize our RAG software suite to predict and design RNA structures and sequences.

AVAILABILITY:

The webserver is freely available online at: http://www.biomath.nyu.edu/ragtop/.

SUPPLEMENTARY INFORMATION:

Supplementary Data, along with usage guidelines, are available at Bioinformatics online.

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