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RNA 3D Structure Comparison Using RNA-Puzzles Toolkit.
Magnus M, Miao Z. Magnus M, et al. Methods Mol Biol. 2023;2586:263-285. doi: 10.1007/978-1-0716-2768-6_16. Methods Mol Biol. 2023. PMID: 36705910
And RNA-Puzzles toolkit is a computational resource derived from RNA-Puzzles, which includes (i) decoy sets generated by different RNA 3D structure prediction methods; (ii) 3D structure normalization, analysis, manipulation, and visualization tools; an …
And RNA-Puzzles toolkit is a computational resource derived from RNA-Puzzles, which includes (i) decoy sets gene …
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. ...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. ...
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 RNA- …
Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challeng …
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 current predictions. …
Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a co …
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 included in this rou
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puz
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.
The stereochemistry of 1052 RNA 3D structures, including 1030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analyzed. The evaluation is based on standards of RNA stereochemistry that the …
The stereochemistry of 1052 RNA 3D structures, including 1030 models predicted by fully automated and human-guided approaches within 22 R
RNA 3D Modeling with FARFAR2, Online.
Watkins AM, Das R. Watkins AM, et al. Methods Mol Biol. 2023;2586:233-249. doi: 10.1007/978-1-0716-2768-6_14. Methods Mol Biol. 2023. PMID: 36705908
Sampling algorithms and energy functions for RNA structure prediction are improving, due to the increasing diversity of structural data available for training statistical potentials and testing structural data, along with a steady supply of blind challenges through the RNA
Sampling algorithms and energy functions for RNA structure prediction are improving, due to the increasing diversity of structural data avai …
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. ...
This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA struc …
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.
34 results