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 Sijenyi; 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

doi:10.1261/rna.031054.111

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

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216 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 language	English
Pages (from-to)	610-625
Number of pages	16
Journal	RNA
Volume	18
Issue number	4
DOIs	https://doi.org/10.1261/rna.031054.111
State	Published - Apr 2012

Keywords

3D prediction
Bioinformatics
Force fields
Structure

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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

@article{125ea3ffcc0f45f186674de5210e5bbb,

title = "RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction",

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.",

keywords = "3D prediction, Bioinformatics, Force fields, Structure",

author = "Cruz, {Jos{\'e} Almeida} and Blanchet, {Marc Fr{\'e}d{\'e}rick} and Michal Boniecki and Bujnicki, {Janusz M.} and Chen, {Shi Jie} and Song Cao and Rhiju Das and Feng Ding and Dokholyan, {Nikolay V.} and Flores, {Samuel Coulbourn} and Lili Huang and Lavender, {Christopher A.} and V{\'e}ronique Lisi and Fran{\c c}ois Major and Katarzyna Mikolajczak and Patel, {Dinshaw J.} and Anna Philips and Tomasz Puton and John Santalucia and Fredrick Sijenyi and Thomas Hermann and Kristian Rother and Magdalena Rother and Alexander Serganov and Marcin Skorupski and Tomasz Soltysinski and Parin Sripakdeevong and Irina Tuszynska and Weeks, {Kevin M.} and Christina Waldsich and Michael Wildauer and Leontis, {Neocles B.} and Eric Westhof",

year = "2012",

month = apr,

doi = "10.1261/rna.031054.111",

language = "English",

volume = "18",

pages = "610--625",

journal = "RNA",

issn = "1355-8382",

number = "4",

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Cruz, JA, Blanchet, MF, Boniecki, M, Bujnicki, JM, Chen, SJ, Cao, S, Das, R, Ding, F, Dokholyan, NV, 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

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 V.

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

Y1 - 2012/4

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.

KW - 3D prediction

KW - Bioinformatics

KW - Force fields

KW - Structure

UR - http://www.scopus.com/inward/record.url?scp=84863338065&partnerID=8YFLogxK

U2 - 10.1261/rna.031054.111

DO - 10.1261/rna.031054.111

M3 - Article

C2 - 22361291

AN - SCOPUS:84863338065

SN - 1355-8382

VL - 18

SP - 610

EP - 625

JO - RNA

JF - RNA

IS - 4

ER -

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

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Keywords

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