RNA SNAPTree

Server for Nucleotide interAction (& 3D structure) Prediction via k-Tree modeling

RNA SNAPTree is a web server to predict RNA nucleotide interactions of all established geometric nomenclatures and families directly from known or predicted canonical base pairs. The information of predicted nucleotide interactions can be directly used to model a 3D conformation as the predicted 3D stucture for the query RNA sequence. The server is build upon BkTree, a command line software package for the same purpose. RNA SNAPTree improves upon BkTree by considering more specific interaction patterns between a single nucleotide and multiple others. It has a user-friendly interface to input an RNA sequence and the canonical base pairs(optional). RNA SNAPTree is maintained on a high performance cluster computer that allows the prediction for RNA sequences up to 250 nucleotides.


Link to RNA SNAPTree

Citation

  • [Ding et al., 2016b] Ding, L., LaMarca, S., Yan, H., Wicker, M., Malmberg, R.L., Momany, C., and Cai, L. (2016) RNA SNAPTree: A Webserver for RNA Nucleotide Interactions and 3D Structure Prediction. in revision.

Related Publication

  • [Ding et al., 2015] Ding, L., Xue, X., LaMarca, S., Mohebbi, M., Samad, A., Malmberg, R.L., Cai, L. (2015) Accurate Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model. Bioinformatics 2015, doi: 10.1093/bioinformatics/btv210.
  • [Ding et al., 2014] Ding, L., Samad, A., Xue, X., Huang, X., Malmberg, R.L., Cai, L. (2014) Stochastic k-tree grammar and its applications in biomolecular structure modeling, Lecture Notes in Computer Science Vol 8370, 308-322.
  • [Ding et al., 2014a] Ding, L., Xue, X., LaMarca, S., Mohebbi, M., Samad, A., Malmberg, R.L., Cai, L. (2014) Ab initio Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model. Proceedings of ECCB'14 Workshop on Computational Methods for Structural RNAs, Strasbourg France, 25-42.