RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

José Almeida Cruz, Marc Frédérick Blanchet, Michal Boniecki, Janusz M. Bujnicki, Shi Jie Chen, Song Cao, Rhiju Das, Feng Ding, Nikolay V. Dokholyan, Samuel Coulbourn Flores, Lili Huang, Christopher A. Lavender, Véronique Lisi, François Major, Katarzyna Mikolajczak, Dinshaw J. Patel, Anna Philips, Tomasz Puton, John Santalucia, Fredrick SijenyiThomas Hermann, Kristian Rother, Magdalena Rother, Alexander Serganov, Marcin Skorupski, Tomasz Soltysinski, Parin Sripakdeevong, Irina Tuszynska, Kevin M. Weeks, Christina Waldsich, Michael Wildauer, Neocles B. Leontis, Eric Westhof

Research output: Contribution to journalArticle

155 Scopus citations

Abstract

We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish (US)
Pages (from-to)610-625
Number of pages16
JournalRNA
Volume18
Issue number4
DOIs
StatePublished - Apr 2012

All Science Journal Classification (ASJC) codes

  • Molecular Biology

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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., ... Westhof, E. (2012). RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA, 18(4), 610-625. https://doi.org/10.1261/rna.031054.111