Group highlights

RNA 3D Structure Comparison Using RNA-Puzzles Toolkit

Magnus, M., & Miao, Z.#

RNA Structure Prediction. Springer US, 263-285 (2023).

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; and (iii) 3D structure comparison metric tools.

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. International Journal of Molecular Sciences.

Gumna J., Antczak M., Adamiak RW., Bujnicki JM., Chen S-J., Ding F., Ghosh P., Li J., Mukherjee S., Nithin C., Pachulska-Wieczorek K., Ponce-Salvatierra A., Popenda M., Sarzynska J., Wirecki T., Zhang D., Zhang S., Zok T., Westhof E., Miao Z.#, Szachniuk M., & Rybarczyk A.#

Int. J. Mol. Sci.23, 9630 (2022).

A computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. They show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5′- and 3′-untranslated regions (UTRs) of the SARS-CoV-2 genome.

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, J. M., Westhof, E., Szachniuk, M. & Miao, Z.#

Nucleic Acids Res. 48, 576–588 (2020).

A computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and standardized datasets), (ii) 3D structure normalization, analysis, manipulation, visualization tools (RNA_format, RNA_normalizer, rna-tools) and (iii) 3D structure comparison metric tools (RNAQUA, MCQ4Structures).

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.#

RNA (2021). doi:10.1261/rna.078685.121.

The evaluation is based on standards of RNA stereochemistry that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity, or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure modeling approaches.

Advances in RNA 3D Structure Modeling Using Experimental Data.

Li, B., Cao, Y., Westhof, E. & Miao, Z.#

Front. Genet. 11:574485, (2020).

They summarize the experiments that can be integrated into RNA structure modeling as well as the computational methods based on these experimental data. We also demonstrate how computational modeling can help the experimental determination of RNA structure. We highlight the recent advances in computational modeling which can offer reliable structure models using high-throughput experimental data.

RNA Structure: Advances and Assessment of 3D Structure Prediction.

Miao, Z.# & Westhof, E.#

Annu. Rev. Biophys. 46, 483–503 (2017).

They hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. They focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. They 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.

 

Full List of publications

(# corresponding author)
Publications from the RNA-Puzzles community can be found on (pubmed).

RNA 3D Structure Comparison Using RNA-Puzzles Toolkit
Magnus, M., & Miao, Z.#
RNA Structure Prediction. Springer US, 263-285 (2023).

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. International Journal of Molecular Sciences.
Gumna J., Antczak M., Adamiak RW., Bujnicki JM., Chen S-J., Ding F., Ghosh P., Li J., Mukherjee S., Nithin C., Pachulska-Wieczorek K., Ponce-Salvatierra A., Popenda M., Sarzynska J., Wirecki T., Zhang D., Zhang S., Zok T., Westhof E., Miao Z.#, Szachniuk M., & Rybarczyk A.#
Int. J. Mol. Sci.23, 9630 (2022).

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, J. M., Westhof, E., Szachniuk, M. & Miao, Z.#
Nucleic Acids Res. 48, 576–588 (2020).

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.#
RNA (2021). doi:10.1261/rna.078685.121.

Advances in RNA 3D Structure Modeling Using Experimental Data.
Li, B., Cao, Y., Westhof, E. & Miao, Z.#
Front. Genet. 11:574485, (2020).

RNA Structure: Advances and Assessment of 3D Structure Prediction.
Miao, Z.# & Westhof, E.#
Annu. Rev. Biophys. 46, 483–503 (2017).

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.
Miao, Z., Adamiak, R. W., Antczak, M., Boniecki, M. J., Bujnicki, J., 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., Piątkowski, 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., Żyła, A., Ren, A., Batey, R. T., Golden, B. L., Huang, L., Lilley, D. M., Liu, Y., Patel, D. J. & Westhof, E.#
RNA 26, 982–995 (2020).

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.
RNA. 2017 May;23(5):655-672.

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.
RNA. 2015 Jun;21(6):1066-84.

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.
RNA. 2012 Apr;18(4):610-25.