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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.

SUBMITTER: Cruz JA 

PROVIDER: S-EPMC3312550 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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

Cruz José Almeida JA   Blanchet Marc-Frédérick MF   Boniecki Michal M   Bujnicki Janusz M JM   Chen Shi-Jie SJ   Cao Song S   Das Rhiju R   Ding Feng F   Dokholyan Nikolay V NV   Flores Samuel Coulbourn SC   Huang Lili L   Lavender Christopher A CA   Lisi Véronique V   Major François F   Mikolajczak Katarzyna K   Patel Dinshaw J DJ   Philips Anna A   Puton Tomasz T   Santalucia John J   Sijenyi Fredrick F   Hermann Thomas T   Rother Kristian K   Rother Magdalena M   Serganov Alexander A   Skorupski Marcin M   Soltysinski Tomasz T   Sripakdeevong Parin P   Tuszynska Irina I   Weeks Kevin M KM   Waldsich Christina C   Wildauer Michael M   Leontis Neocles B NB   Westhof Eric E  

RNA (New York, N.Y.) 20120223 4

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 app  ...[more]

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