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Items: 1 to 20 of 93

1.

Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking.

Kappel K, Das R.

Structure. 2019 Jan 2;27(1):140-151.e5. doi: 10.1016/j.str.2018.10.001. Epub 2018 Nov 8.

PMID:
30416038
2.

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes.

Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R.

Nat Methods. 2018 Nov;15(11):947-954. doi: 10.1038/s41592-018-0172-2. Epub 2018 Oct 30.

PMID:
30377372
3.

Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes.

Nithin C, Ghosh P, Bujnicki JM.

Genes (Basel). 2018 Aug 25;9(9). pii: E432. doi: 10.3390/genes9090432. Review.

5.

Simultaneous prediction of protein folding and docking at high resolution.

Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D.

Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18978-83. doi: 10.1073/pnas.0904407106. Epub 2009 Oct 28.

6.

DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking.

Tuszynska I, Bujnicki JM.

BMC Bioinformatics. 2011 Aug 18;12:348. doi: 10.1186/1471-2105-12-348.

7.

Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis.

Parks JW, Kappel K, Das R, Stone MD.

RNA. 2017 Feb;23(2):175-188. doi: 10.1261/rna.058743.116. Epub 2016 Nov 15.

8.

Computational modeling of protein-RNA complex structures.

Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski LP, Dunin-Horkawicz S, Bujnicki JM.

Methods. 2014 Feb;65(3):310-9. doi: 10.1016/j.ymeth.2013.09.014. Epub 2013 Sep 29. Review.

PMID:
24083976
9.

RNA folding pathways and the self-assembly of ribosomes.

Woodson SA.

Acc Chem Res. 2011 Dec 20;44(12):1312-9. doi: 10.1021/ar2000474. Epub 2011 Jun 29.

10.

Blind tests of RNA-protein binding affinity prediction.

Kappel K, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D, Das R.

Proc Natl Acad Sci U S A. 2019 Apr 8. pii: 201819047. doi: 10.1073/pnas.1819047116. [Epub ahead of print]

PMID:
30962376
11.

Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts.

Sripakdeevong P, Cevec M, Chang AT, Erat MC, Ziegeler M, Zhao Q, Fox GE, Gao X, Kennedy SD, Kierzek R, Nikonowicz EP, Schwalbe H, Sigel RK, Turner DH, Das R.

Nat Methods. 2014 Apr;11(4):413-6. doi: 10.1038/nmeth.2876. Epub 2014 Mar 2.

12.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug;10(4):040301. Epub 2013 Aug 2.

PMID:
23912807
14.

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27.

Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ.

Proteins. 2013 Dec;81(12):2201-9. doi: 10.1002/prot.24425. Epub 2013 Oct 17.

15.

RNA recognition by RNP proteins during RNA processing.

Varani G, Nagai K.

Annu Rev Biophys Biomol Struct. 1998;27:407-45. Review.

PMID:
9646873
16.

Spliceosome structure and function.

Will CL, Lührmann R.

Cold Spring Harb Perspect Biol. 2011 Jul 1;3(7). pii: a003707. doi: 10.1101/cshperspect.a003707. Review.

17.

High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly.

McGinnis JL, Duncan CD, Weeks KM.

Methods Enzymol. 2009;468:67-89. doi: 10.1016/S0076-6879(09)68004-6.

18.

Programmable design of functional ribonucleoprotein complexes.

Rath AK, Kellermann SJ, Rentmeister A.

Chem Asian J. 2014 Aug;9(8):2045-51. doi: 10.1002/asia.201402220. Epub 2014 Jun 4.

PMID:
24895170
19.

Assessment and challenges of ligand docking into comparative models of G-protein coupled receptors.

Nguyen ED, Norn C, Frimurer TM, Meiler J.

PLoS One. 2013 Jul 2;8(7):e67302. doi: 10.1371/journal.pone.0067302. Print 2013.

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