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2020

Miao Z, Adamiak R W, Antczak M, Boniecki M J, Bujnicki J M, Chen S J, Cheng C Y, Cheng Y, Chou F C, Das R, Dokholyan N V, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann T H, Piatkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins A M, Wiedemann J, Xiao Y, Xu X, Yesselman J D, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Zyla A, Ren A, Batey R T, Golden B L, Huang L, Lilley D M, Liu Y, Patel D J, Westhof E

RNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers Journal Article

In: RNA, vol. 26, no. 8, pp. 982-995, 2020, ISBN: 32371455.

Abstract | Links | BibTeX | Tags: RNA structure aptamer modeing prediction ribozyme, Unité ARN, WESTHOF

@article{,

title = {RNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers},

author = {Z Miao and R W Adamiak and M Antczak and M J Boniecki and J M Bujnicki and S J Chen and C Y Cheng and Y Cheng and F C Chou and R Das and N V Dokholyan and F Ding and C Geniesse and Y Jiang and A Joshi and A Krokhotin and M Magnus and O Mailhot and F Major and T H Mann and P Piatkowski and R Pluta and M Popenda and J Sarzynska and L Sun and M Szachniuk and S Tian and J Wang and J Wang and A M Watkins and J Wiedemann and Y Xiao and X Xu and J D Yesselman and D Zhang and Y Zhang and Z Zhang and C Zhao and P Zhao and Y Zhou and T Zok and A Zyla and A Ren and R T Batey and B L Golden and L Huang and D M Lilley and Y Liu and D J Patel and E Westhof},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32371455?dopt=Abstract},

doi = {10.1261/rna.075341.120},

isbn = {32371455},

year  = {2020},

date = {2020-01-01},

journal = {RNA},

volume = {26},

number = {8},

pages = {982-995},

abstract = {RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. We now report the prediction of six RNA sequences: four structures of nucleolytic ribozymes and two of riboswitches. Systematic protocols for comparing models and crystal structures are described and analyzed. In these six puzzles, we discuss a) the comparison between the automated web server and human experts; b) the prediction of coaxial stacking; c) the prediction of structural details and ligand binding; d) the development of novel prediction methods; and e) the potential improvements to be made. It is illustrated that correct coaxial stacking and tertiary contacts are key for the prediction of RNA architecture, while ligand binding modes can be only predicted with low resolution and accurate ligand binding prediction still remains out of reach. All the predicted models are available for the future development of force field parameters and the improvement of comparison and assessment tools.},

keywords = {RNA structure aptamer modeing prediction ribozyme, Unité ARN, WESTHOF},

pubstate = {published},

tppubtype = {article}

}

Group leader

Pascale ROMBY