Grace Meng1, Marva Tariq2, Swati Jain1, Shereef Elmetwaly1, Tamar Schlick1,3,4. 1. Department of Chemistry, New York University, New York, NY 10003, USA. 2. Department of Chemistry, Smith College, Northampton, MA 01063, USA. 3. Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA. 4. NYU-ECNU Center for Computational Chemistry at New York University Shanghai, Shanghai 3663, China.
Abstract
SUMMARY: 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 AND IMPLEMENTATION: The webserver is freely available online at: http://www.biomath.nyu.edu/ragtop/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: 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 AND IMPLEMENTATION: The webserver is freely available online at: http://www.biomath.nyu.edu/ragtop/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Namhee Kim; Christian Laing; Shereef Elmetwaly; Segun Jung; Jeremy Curuksu; Tamar Schlick Journal: Proc Natl Acad Sci U S A Date: 2014-03-03 Impact factor: 11.205
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