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References

  1. N. Kim, C. Laing, S. Elmetwaly, S. Jung, J. Curuksu, and Schlick, T. (2014) Graph-based sampling for approximating global helical topologies of RNA. Proc Natl Acad Sci USA, 111(11), 4079-4084.

  2. C. S. Bayrak, N. Kim, and T. Schlick. (2017) Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction. Nucleic Acids Res, 45(9), 5414-5422.

  3. S. Jain, and T. Schlick. (2017). F-RAG: Generating atomic coordinates from RNA graphs by fragment assembly. J Mol Biol, 429(23), 3587-3605.

  4. S. Jain, A. Laederach, S. B. V. Ramos, and T. Schlick. (2018). A pipeline for computational design of novel RNA-like topologies. Nucleic Acids Res, 46(14), 7040-7051

  5. D. Fera, N. Kim, N. Shiffeldrim, J. Zorn, U. Laserson, H. H. Gan, and T. Schlick. (2004) RAG: RNA-As-Graphs web resource. BMC Bioinformatics, 5(1), 88.

  6. H. H. Gan, S. Pasquali, and T. Schlick. (2003) Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res, 31(11), 2926-2943.

  7. H. H. Gan, D. Fera, J. Zorn, N. Shiffeldrim, M. Tang, U. Laserson, ... and T. Schlick. (2004). RAG: RNA-As-Graphs database-concepts, analysis, and features. Bioinformatics, 20(8), 1285-1291.

  8. N. Kim, L. Petingi, and T. Schlick. (2013) Network theory tools for RNA modeling. WSEAS Trans Math, 9(12), 941-955.

  9. N. Kim, N. Shiffeldrim, H. H. Gan, and T. Schlick. (2004) Candidates for novel RNA topologies. J Mol Biol, 341(5), 1129-1144.

  10. N. Baba, S. Elmetwaly, N. Kim, and T. Schlick. (2016) Predicting large RNA-Like topologies by a knowledge-based clustering approach. J Mol Biol, 428(5), 811-821.

  11. C. Laing, D. Wen, J. T. Wang, and T. Schlick. (2012). Predicting coaxial helical stacking in RNA junctions. Nucleic Acids Res, 40(2), 487-498.

  12. C. Laing, S. Jung, N. Kim, S. Elmetwaly, M. Zahran, and T. Schlick. (2013). Predicting helical topologies in RNA junctions as tree graphs. PloS one, 8(8), e71947.

  13. M. Zahran, C. S. Bayrak, S. Elmetwaly, and T. Schlick. (2015) RAG-3D: a search tool for RNA 3D substructures. Nucleic Acids Res, 43(19), gkv823-9488.

  14. N. Kim, Z. Zheng, S. Elmetwaly, and T. Schlick. (2014) RNA graph partitioning for the discovery of RNA modularity: a novel application of graph partition algorithm to biology. PLoS one, 9(9), e106074.

  15. R. Lorenz, S. H. Bernhart, C. H. Zu Siederdissen, H. Tafer, C. Flamm, P. F. Stadler, and I. L. Hofacker. (2011). ViennaRNA Package 2.0. Algorithms for Molecular Biology, 6(1), 26.

  16. R. M. Dirks, and N. A. Pierce. (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots. J Comp Chem, 24(13), 1664-1677.

  17. R. M. Dirks, and N. A. Pierce. (2004) An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J Comp Chem, 25(10), 1295-1304.

  18. R. M. Dirks, J. S. Bois, J. M. Schaeffer, E. Winfree, and N. A. Pierce. (2007). Thermodynamic analysis of interacting nucleic acid strands. SIAM review, 49(1), 65-88.