Using 3dRNA for RNA 3‐D Structure Prediction and Evaluation

Jian Wang1, Yi Xiao1

1 Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 5.9
DOI:  10.1002/cpbi.21
Online Posting Date:  May, 2017
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This unit describes how to use 3dRNA to predict RNA 3‐D structures from their sequences and secondary (2‐D) structures, and how to use 3dRNAscore to evaluate the predicted structures. The predicted RNA 3‐D structures can be used to predict or understand their functions and can also be used to find the interactions between the RNA and other molecules. © 2017 by John Wiley & Sons, Inc.

Keywords: 3dRNA; 3dRNAscore; RNA; 3‐D structure prediction; 3‐D structure evaluation

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Table of Contents

  • Introduction
  • Basic Protocol 1: RNA 3‐D Structure Prediction Using the 3dRNA Web Server
  • Basic Protocol 2: RNA 3‐D Structure Evaluation Using the 3dRNAscore Web Server
  • Alternate Protocol 1: Accessing 3dRNA and 3dRNAscore Server Remotely
  • Alternate Protocol 2: Using 3dRNA and 3dRNAscore Locally
  • Support Protocol 1: Installing NSP
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

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  Cruz, J.A., Blanchet, M.F., Boniecki, M., Bujnicki, J.M., Chen, S.J., Cao, S., Das, R., Ding, F., Dokholyan, N.V., Flores, S.C., Huang, L., Lavender, C.A., Lisi, V., Major, F., Mikolajczak, K., Patel, D.J., Philips, A., Puton, T., Santalucia, J., Sijenyi, F., Hermann, T., Rother, K., Rother, M., Serganov, A., Skorupski, M., Soltysinski, T., Sripakdeevong, P., Tuszynska, I., Weeks, K.M., Waldsich, C., Wildauer, M., Leontis, N.B., and Westhof, E. 2012. RNA‐Puzzles: A CASP‐like evaluation of RNA three‐dimensional structure prediction. RNA 18:610‐625. doi: 10.1261/rna.031054.111.
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  Massire, C. and Westhof, E. 1998. MANIP: An interactive tool for modelling RNA. J. Mol. Graph. Model. 16:197‐205, 255‐197. doi: 10.1016/S1093‐3263(98)80004‐1.
  Miao, Z., Adamiak, R.W., Blanchet, M.F., Boniecki, M., Bujnicki, J.M., Chen, S.J., Cheng, C., Chojnowski, G., Chou, F.C., Cordero, P., Cruz, J.A., Ferre‐D'Amare, A.R., Das, R., Ding, F., Dokholyan, N.V., Dunin‐Horkawicz, S., Kladwang, W., Krokhotin, A., Lach, G., Magnus, M., Major, F., Mann, T.H., Masquida, B., Matelska, D., Meyer, M., Peselis, A., Popenda, M., Purzycka, K.J., Serganov, A., Stasiewicz, J., Szachniuk, M., Tandon, A., Tian, S., Wang, J., Xiao, Y., Xu, X., Zhang, J., Zhao, P., Zok, T., and Westhof, E. 2015. RNA‐Puzzles Round II: Assessment of RNA structure prediction programs applied to three large RNA structures. RNA 21:1066‐1084. doi: 10.1261/rna.049502.114.
  Parisien, M. and Major, F. 2008. The MC‐Fold and MC‐Sym pipeline infers RNA structure from sequence data. Nature 452:51‐55. doi: 10.1038/nature06684.
  Rother, M., Rother, K., Puton, T., and Bujnicki, J.M. 2011. ModeRNA: A tool for comparative modeling of RNA 3D structure. Nucleic Acids Res. 39:4007‐4022. doi: 10.1093/nar/gkq1320.
  Sharma, S., Ding, F., and Dokholyan, N.V. 2008. iFoldRNA: Three‐dimensional RNA structure prediction and folding. Bioinformatics 24:1951‐1952. doi: 10.1093/bioinformatics/btn328.
  Shi, Y.Z., Wang, F.H., Wu, Y.Y., and Tan, Z.J. 2014. A coarse‐grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect. J. Chem. Phys. 141:105102. doi: 10.1063/1.4894752.
  Wang, J., Zhao, Y., Zhu, C., and Xiao, Y. 2015. 3dRNAscore: A distance and torsion angle dependent evaluation function of 3D RNA structures. Nucleic Acids Res. 43:e63. doi: 10.1093/nar/gkv141.
  Xu, X.J., Zhao, P.N., and Chen, S.J. 2014. Vfold: A Web server for RNA structure and folding thermodynamics prediction. Plos One 9:e107504. doi: 10.1371/journal.pone.0107504.
  Zhao, Y., Gong, Z., and Xiao, Y. 2011. Improvements of the hierarchical approach for predicting RNA tertiary structure. J. Biomol. Struct. Dyn. 28:815‐826. doi: 10.1080/07391102.2011.10508609.
  Zhao, Y., Huang, Y., Gong, Z., Wang, Y., Man, J., and Xiao, Y. 2012. Automated and fast building of three‐dimensional RNA structures. Sci. Rep. 2:734. doi: 10.1038/srep00734.
Key Reference
  Zhao et al., 2012. See above.
  This reference describes the implementation of 3dRNA.
  Wang et al., 2015. See above.
  This reference describes the implementation of 3dRNAscore.
Internet Resources
  3dRNA Web site for RNA 3‐D structure prediction.
  3dRNAscore Web site for RNA 3‐D structure scoring.
  The project of NSP including the source codes and the documentation.
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