The RNA-As-Graphs Topology (RAGTOP) software suite is developed in the lab of Prof. Tamar Schlick at New York University. The different features offered by this software include representing RNA secondary structure as three-dimensional tree graphs and sampling different graph topologies [3, 4]; fragment assembly for RNA graphs (F-RAG) to generate 3D atomic models of RNA for graphs [5], and design of sequences to fold onto RNA-like tree graph topologies [6].

Copyright Statement:

The RAGTOP software suite was developed in the lab of Prof. Tamar Schlick at New York University. The package is provided for use in research purposes only; for other applications please contact Prof. Tamar Schlick. We require everyone who publishes or presents results from RAGTOP to please cite our program, names of individual components, and associated original publications, as below:

Citation Requirements:

Please cite the papers below when using RAGTOP. Papers 1 and 2 are for RAGTOP's JunctionExplorer component to predict coaxial stacking and family for 3-way and 4-way junctions; papers 3 and 4 are for RAGTOP's Monte Carlo/Simulated Annealing component to sample 3D tree graph topologies; and papers 5 and 6 are for RAGTOP's F-RAG component to generate atomic models for RNA 3D structure prediction and design of RNA-like topologies.

  1. C. Laing, D. Wen, J. T. L. Wang, and T. Schlick, "Predicting coaxial helical stacking in RNA junctions.," Nucleic Acids Res, vol. 40, no. 2, pp. 487-498, 2012
  2. C. Laing, S. Jung, N. Kim, S. Elmetwaly, M. Zahran, and T. Schlick, "Predicting helical topologies in RNA junctions as tree graphs," PLoS ONE, vol. 8, no. 8, p. e71947, 2013
  3. N. Kim, C. Laing, S. Elmetwaly, S. Jung, J. Curuksu, and T. Schlick, "Graph-based sampling for approximating global helical topologies of RNA", Proc Natl Acad Sci USA, vol. 111, no. 11, pp. 4079-4084, 2014
  4. C. S. Bayrak, N. Kim, and T. Schlick, "Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction.," Nucleic Acids Res, vol. 45, no. 9, pp. 5414-5422, 2017
  5. S. Jain and T. Schlick, "F-RAG: Generating atomic models from RNA graphs using fragment assembly," J Mol Biol, vol. 429, no. 23, pp. 3587-3605, 2017
  6. S. Jain, A. Laederach, S. B. Ramos, and T. Schlick, "A pipeline for computational design of novel RNA-like topologies," Nucleic Acid Res, (In Revision), 2018


  1. Download and untar the package: tar zxvf <package_name>
  2. Change directory: cd <package_directory>
  3. Example: To run MC/SA: ./RAGTOP -mcrun -file 1DK1 -inputdir Examples/MCRun/Input/ -outputdir Examples/MCRun/Output/

Please check the Manual for more details


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For questions or comments, please contact the RAG team