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Items: 1 to 20 of 265

1.

RNAmap2D - calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures.

Pietal MJ, Szostak N, Rother KM, Bujnicki JM.

BMC Bioinformatics. 2012 Dec 21;13:333. doi: 10.1186/1471-2105-13-333.

2.

PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure.

Pietal MJ, Tuszynska I, Bujnicki JM.

Bioinformatics. 2007 Jun 1;23(11):1429-30. Epub 2007 Mar 30.

3.

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

Jossinet F, Ludwig TE, Westhof E.

Bioinformatics. 2010 Aug 15;26(16):2057-9. doi: 10.1093/bioinformatics/btq321. Epub 2010 Jun 18.

4.
5.

A novel protocol for three-dimensional structure prediction of RNA-protein complexes.

Huang Y, Liu S, Guo D, Li L, Xiao Y.

Sci Rep. 2013;3:1887. doi: 10.1038/srep01887.

6.

ModeRNA server: an online tool for modeling RNA 3D structures.

Rother M, Milanowska K, Puton T, Jeleniewicz J, Rother K, Bujnicki JM.

Bioinformatics. 2011 Sep 1;27(17):2441-2. doi: 10.1093/bioinformatics/btr400. Epub 2011 Jul 4.

7.

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures.

Popenda M, Szachniuk M, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW.

BMC Bioinformatics. 2010 May 6;11:231. doi: 10.1186/1471-2105-11-231.

8.

Quantitative analysis of nucleic acid three-dimensional structures.

Gendron P, Lemieux S, Major F.

J Mol Biol. 2001 May 18;308(5):919-36.

PMID:
11352582
9.

PDA: an automatic and comprehensive analysis program for protein-DNA complex structures.

Kim R, Guo JT.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S13. doi: 10.1186/1471-2164-10-S1-S13.

10.

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

Olechnovič K, Venclovas C.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W259-63. doi: 10.1093/nar/gku294. Epub 2014 May 16.

11.

Tools for the automatic identification and classification of RNA base pairs.

Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E.

Nucleic Acids Res. 2003 Jul 1;31(13):3450-60.

12.

RNA tertiary structure prediction with ModeRNA.

Rother M, Rother K, Puton T, Bujnicki JM.

Brief Bioinform. 2011 Nov;12(6):601-13. doi: 10.1093/bib/bbr050. Epub 2011 Sep 6.

13.

MetalionRNA: computational predictor of metal-binding sites in RNA structures.

Philips A, Milanowska K, Lach G, Boniecki M, Rother K, Bujnicki JM.

Bioinformatics. 2012 Jan 15;28(2):198-205. doi: 10.1093/bioinformatics/btr636. Epub 2011 Nov 21.

14.

Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure.

Reinharz V, Major F, Waldispühl J.

Bioinformatics. 2012 Jun 15;28(12):i207-14. doi: 10.1093/bioinformatics/bts226.

15.

NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules.

Hamdani HY, Appasamy SD, Willett P, Artymiuk PJ, Firdaus-Raih M.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W35-41. doi: 10.1093/nar/gks513. Epub 2012 May 31.

16.

Efficient RNA pairwise structure comparison by SETTER method.

Hoksza D, Svozil D.

Bioinformatics. 2012 Jul 15;28(14):1858-64. doi: 10.1093/bioinformatics/bts301. Epub 2012 May 18.

17.

Nucleic acid visualization with UCSF Chimera.

Couch GS, Hendrix DK, Ferrin TE.

Nucleic Acids Res. 2006 Feb 14;34(4):e29.

18.

ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes.

Waleń T, Chojnowski G, Gierski P, Bujnicki JM.

Nucleic Acids Res. 2014 Oct 29;42(19):e151. doi: 10.1093/nar/gku765. Epub 2014 Aug 26.

19.
20.

Computational structure analysis of biomacromolecule complexes by interface geometry.

Mahdavi S, Salehzadeh-Yazdi A, Mohades A, Masoudi-Nejad A.

Comput Biol Chem. 2013 Dec;47:16-23. doi: 10.1016/j.compbiolchem.2013.06.003. Epub 2013 Jun 25.

PMID:
23850846
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