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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 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-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 …
RNA 3D structure prediction guided by independent folding of homologous sequences.
Magnus M, Kappel K, Das R, Bujnicki JM. Magnus M, et al. BMC Bioinformatics. 2019 Oct 22;20(1):512. doi: 10.1186/s12859-019-3120-y. BMC Bioinformatics. 2019. PMID: 31640563 Free PMC article.
The prediction of tertiary structures of complex RNAs is still a challenging task. RESULTS: Using the observation that RNA sequences from the same RNA family fold into conserved structure, we test herein whether parallel modeling of RNA homologs can improve a …
The prediction of tertiary structures of complex RNAs is still a challenging task. RESULTS: Using the observation that RNA sequences …
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 …
Not Only Mutations Matter: Molecular Picture of Acute Myeloid Leukemia Emerging from Transcriptome Studies.
Handschuh L. Handschuh L. J Oncol. 2019 Jul 30;2019:7239206. doi: 10.1155/2019/7239206. eCollection 2019. J Oncol. 2019. PMID: 31467542 Free PMC article. Review.
However, transcriptome is not limited to the protein-coding genes; other types of RNA molecules exist in a cell and regulate genome function. It was shown that microRNA (miRNA) profiles differentiated AML groups and predicted outcome not worse than protein-coding gene prof …
However, transcriptome is not limited to the protein-coding genes; other types of RNA molecules exist in a cell and regulate genome f …
FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds.
Watkins AM, Rangan R, Das R. Watkins AM, et al. Structure. 2020 Aug 4;28(8):963-976.e6. doi: 10.1016/j.str.2020.05.011. Epub 2020 Jun 11. Structure. 2020. PMID: 32531203
Predicting RNA three-dimensional structures from sequence could accelerate understanding of the growing number of RNA molecules being discovered across biology. ...In 16 of 21 RNA-Puzzles revisited without experimental data or expert intervention, FARF …
Predicting RNA three-dimensional structures from sequence could accelerate understanding of the growing number of RNA molecule …
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