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 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 Sijenyi & 13 others Thomas 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

139 Citations (Scopus)

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 1 2012

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RNA

All Science Journal Classification (ASJC) codes

  • Molecular Biology

Cite this

Cruz, J. A., Blanchet, M. F., Boniecki, M., Bujnicki, J. M., Chen, S. J., Cao, S., ... 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
Cruz, José Almeida ; Blanchet, Marc Frédérick ; Boniecki, Michal ; Bujnicki, Janusz M. ; Chen, Shi Jie ; Cao, Song ; Das, Rhiju ; Ding, Feng ; Dokholyan, Nikolay ; Flores, Samuel Coulbourn ; Huang, Lili ; Lavender, Christopher A. ; Lisi, Véronique ; Major, François ; Mikolajczak, Katarzyna ; Patel, Dinshaw J. ; Philips, Anna ; Puton, Tomasz ; Santalucia, John ; Sijenyi, Fredrick ; Hermann, Thomas ; Rother, Kristian ; Rother, Magdalena ; Serganov, Alexander ; Skorupski, Marcin ; Soltysinski, Tomasz ; Sripakdeevong, Parin ; Tuszynska, Irina ; Weeks, Kevin M. ; Waldsich, Christina ; Wildauer, Michael ; Leontis, Neocles B. ; Westhof, Eric. / RNA-Puzzles : A CASP-like evaluation of RNA three-dimensional structure prediction. In: RNA. 2012 ; Vol. 18, No. 4. pp. 610-625.
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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.",
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Cruz, JA, Blanchet, MF, Boniecki, M, Bujnicki, JM, Chen, SJ, Cao, S, Das, R, Ding, F, Dokholyan, N, Flores, SC, Huang, L, Lavender, CA, Lisi, V, Major, F, Mikolajczak, K, Patel, DJ, 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, KM, Waldsich, C, Wildauer, M, Leontis, NB & Westhof, E 2012, 'RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction', RNA, vol. 18, no. 4, pp. 610-625. https://doi.org/10.1261/rna.031054.111

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

In: RNA, Vol. 18, No. 4, 01.04.2012, p. 610-625.

Research output: Contribution to journalArticle

TY - JOUR

T1 - RNA-Puzzles

T2 - A CASP-like evaluation of RNA three-dimensional structure prediction

AU - Cruz, José Almeida

AU - Blanchet, Marc Frédérick

AU - Boniecki, Michal

AU - Bujnicki, Janusz M.

AU - Chen, Shi Jie

AU - Cao, Song

AU - Das, Rhiju

AU - Ding, Feng

AU - Dokholyan, Nikolay

AU - Flores, Samuel Coulbourn

AU - Huang, Lili

AU - Lavender, Christopher A.

AU - Lisi, Véronique

AU - Major, François

AU - Mikolajczak, Katarzyna

AU - Patel, Dinshaw J.

AU - Philips, Anna

AU - Puton, Tomasz

AU - Santalucia, John

AU - Sijenyi, Fredrick

AU - Hermann, Thomas

AU - Rother, Kristian

AU - Rother, Magdalena

AU - Serganov, Alexander

AU - Skorupski, Marcin

AU - Soltysinski, Tomasz

AU - Sripakdeevong, Parin

AU - Tuszynska, Irina

AU - Weeks, Kevin M.

AU - Waldsich, Christina

AU - Wildauer, Michael

AU - Leontis, Neocles B.

AU - Westhof, Eric

PY - 2012/4/1

Y1 - 2012/4/1

N2 - 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.

AB - 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.

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U2 - 10.1261/rna.031054.111

DO - 10.1261/rna.031054.111

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JF - RNA

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Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S et al. RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA. 2012 Apr 1;18(4):610-625. https://doi.org/10.1261/rna.031054.111