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Items: 13

1.

RNA 3D structure prediction guided by independent folding of homologous sequences.

Magnus M, Kappel K, Das R, Bujnicki JM.

BMC Bioinformatics. 2019 Oct 22;20(1):512. doi: 10.1186/s12859-019-3120-y.

2.

All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State.

Zhang T, Hu G, Yang Y, Wang J, Zhou Y.

J Comput Biol. 2019 Oct 23. doi: 10.1089/cmb.2019.0251. [Epub ahead of print]

PMID:
31638408
3.

Not Only Mutations Matter: Molecular Picture of Acute Myeloid Leukemia Emerging from Transcriptome Studies.

Handschuh L.

J Oncol. 2019 Jul 30;2019:7239206. doi: 10.1155/2019/7239206. eCollection 2019. Review.

4.

QRNAS: software tool for refinement of nucleic acid structures.

Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM.

BMC Struct Biol. 2019 Mar 21;19(1):5. doi: 10.1186/s12900-019-0103-1.

5.

LCS-TA to identify similar fragments in RNA 3D structures.

Wiedemann J, Zok T, Milostan M, Szachniuk M.

BMC Bioinformatics. 2017 Oct 23;18(1):456. doi: 10.1186/s12859-017-1867-6.

6.

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

Miao Z, Westhof E.

Annu Rev Biophys. 2017 May 22;46:483-503. doi: 10.1146/annurev-biophys-070816-034125. Epub 2017 Mar 30. Review.

PMID:
28375730
7.

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. doi: 10.1261/rna.060368.116. Epub 2017 Jan 30.

8.

RNAssess--a web server for quality assessment of RNA 3D structures.

Lukasiak P, Antczak M, Ratajczak T, Szachniuk M, Popenda M, Adamiak RW, Blazewicz J.

Nucleic Acids Res. 2015 Jul 1;43(W1):W502-6. doi: 10.1093/nar/gkv557. Epub 2015 Jun 11.

9.

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. doi: 10.1261/rna.049502.114. Epub 2015 Apr 16.

10.

Modeling complex RNA tertiary folds with Rosetta.

Cheng CY, Chou FC, Das R.

Methods Enzymol. 2015;553:35-64. doi: 10.1016/bs.mie.2014.10.051. Epub 2015 Feb 12.

PMID:
25726460
11.

RNA 3D structure prediction by using a coarse-grained model and experimental data.

Xia Z, Bell DR, Shi Y, Ren P.

J Phys Chem B. 2013 Mar 21;117(11):3135-44. doi: 10.1021/jp400751w. Epub 2013 Mar 11.

PMID:
23438338
12.

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. doi: 10.1261/rna.031054.111. Epub 2012 Feb 23.

13.

Four small puzzles that Rosetta doesn't solve.

Das R.

PLoS One. 2011;6(5):e20044. doi: 10.1371/journal.pone.0020044. Epub 2011 May 20.

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