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RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.
Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Piątkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins AM, Wiedemann J, Xiao Y, Xu X, Yesselman JD, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Żyła A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E. Miao Z, et al. RNA. 2020 Aug;26(8):982-995. doi: 10.1261/rna.075341.120. Epub 2020 May 5. RNA. 2020. PMID: 32371455 Free PMC article.
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. ...We now report the prediction of 3D structures for six RNA sequences: four nucleolytic ribozymes and two riboswitches. ...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. ...We
RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.
Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z. Magnus M, et al. Nucleic Acids Res. 2020 Jan 24;48(2):576-588. doi: 10.1093/nar/gkz1108. Nucleic Acids Res. 2020. PMID: 31799609 Free PMC article.
Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challenges of RNA-Puzzles, a community-wide effort on the assessment of blind prediction of RNA tertiary structures. The …
Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding c …
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.
Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B 2nd, Xiao Y, Xu X, Zhang D, Zok T, Westhof E. Miao Z, et al. RNA. 2017 May;23(5):655-672. doi: 10.1261/rna.060368.116. Epub 2017 Jan 30. RNA. 2017. PMID: 28138060 Free PMC article.
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are includ
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA
RNA Structure: Advances and Assessment of 3D Structure Prediction.
Miao Z, Westhof E. Miao Z, et al. Annu Rev Biophys. 2017 May 22;46:483-503. doi: 10.1146/annurev-biophys-070816-034125. Epub 2017 Mar 30. Annu Rev Biophys. 2017. PMID: 28375730 Review.
Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of curren …
Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which …
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E. Miao Z, et al. RNA. 2015 Jun;21(6):1066-84. doi: 10.1261/rna.049502.114. Epub 2015 Apr 16. RNA. 2015. PMID: 25883046 Free PMC article.
This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with l …
This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA
Advances in RNA 3D Structure Modeling Using Experimental Data.
Li B, Cao Y, Westhof E, Miao Z. Li B, et al. Front Genet. 2020 Oct 26;11:574485. doi: 10.3389/fgene.2020.574485. eCollection 2020. Front Genet. 2020. PMID: 33193680 Free PMC article. Review.
RNAs adopt specific three-dimensional conformations to enable their functions. Experimental determination of high-resolution RNA structures using x-ray crystallography is both laborious and demands expertise, thus, hindering our comprehension of RNA structural biolo …
RNAs adopt specific three-dimensional conformations to enable their functions. Experimental determination of high-resolution RNA stru …
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions.
Carrascoza F, Antczak M, Miao Z, Westhof E, Szachniuk M. Carrascoza F, et al. RNA. 2022 Feb;28(2):250-262. doi: 10.1261/rna.078685.121. Epub 2021 Nov 24. RNA. 2022. PMID: 34819324 Free PMC article.
In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models predicted using dedicated …
In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary s …
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.
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. Cruz JA, et al. RNA. 2012 Apr;18(4):610-25. doi: 10.1261/rna.031054.111. Epub 2012 Feb 23. RNA. 2012. PMID: 22361291 Free PMC article.
We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. ...We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA
We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three …
Entanglements of structure elements revealed in RNA 3D models.
Popenda M, Zok T, Sarzynska J, Korpeta A, Adamiak RW, Antczak M, Szachniuk M. Popenda M, et al. Nucleic Acids Res. 2021 Sep 27;49(17):9625-9632. doi: 10.1093/nar/gkab716. Nucleic Acids Res. 2021. PMID: 34432024 Free PMC article.
RNA-Puzzles datasets, subjected to multi-criteria analysis, allow revealing the strengths and weaknesses of computer prediction methods. ...Our computational pipeline for entanglement detection, applied for 1,017 non-redundant models from RNA-Puzzles,
RNA-Puzzles datasets, subjected to multi-criteria analysis, allow revealing the strengths and weaknesses of computer predictio
RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks.
Singh J, Paliwal K, Singh J, Zhou Y. Singh J, et al. J Chem Inf Model. 2021 Jun 28;61(6):2610-2622. doi: 10.1021/acs.jcim.1c00153. Epub 2021 May 26. J Chem Inf Model. 2021. PMID: 34037398
Here, we employed the dilated convolutional neural network to predict backbone torsion and pseudotorsion angles using a single RNA sequence as input. The method called SPOT-RNA-1D was trained on a high-resolution training data set and tested on three independent, no …
Here, we employed the dilated convolutional neural network to predict backbone torsion and pseudotorsion angles using a single RNA se …
26 results