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Items: 1 to 20 of 163

1.

PRIDB: a Protein-RNA interface database.

Lewis BA, Walia RR, Terribilini M, Ferguson J, Zheng C, Honavar V, Dobbs D.

Nucleic Acids Res. 2011 Jan;39(Database issue):D277-82. doi: 10.1093/nar/gkq1108. Epub 2010 Nov 11.

2.

RNABindR: a server for analyzing and predicting RNA-binding sites in proteins.

Terribilini M, Sander JD, Lee JH, Zaback P, Jernigan RL, Honavar V, Dobbs D.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W578-84. Epub 2007 May 5.

3.

NPIDB: Nucleic acid-Protein Interaction DataBase.

Kirsanov DD, Zanegina ON, Aksianov EA, Spirin SA, Karyagina AS, Alexeevski AV.

Nucleic Acids Res. 2013 Jan;41(Database issue):D517-23. doi: 10.1093/nar/gks1199. Epub 2012 Nov 27.

4.

Prediction of RNA binding sites in proteins from amino acid sequence.

Terribilini M, Lee JH, Yan C, Jernigan RL, Honavar V, Dobbs D.

RNA. 2006 Aug;12(8):1450-62. Epub 2006 Jun 21.

5.

JAIL: a structure-based interface library for macromolecules.

G√ľnther S, von Eichborn J, May P, Preissner R.

Nucleic Acids Res. 2009 Jan;37(Database issue):D338-41. doi: 10.1093/nar/gkn599. Epub 2008 Oct 2.

6.

Predicting RNA-protein interactions using only sequence information.

Muppirala UK, Honavar VG, Dobbs D.

BMC Bioinformatics. 2011 Dec 22;12:489. doi: 10.1186/1471-2105-12-489.

7.

SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces.

Teyra J, Doms A, Schroeder M, Pisabarro MT.

BMC Bioinformatics. 2006 Mar 2;7:104.

8.
9.

HotSprint: database of computational hot spots in protein interfaces.

Guney E, Tuncbag N, Keskin O, Gursoy A.

Nucleic Acids Res. 2008 Jan;36(Database issue):D662-6. Epub 2007 Oct 24.

10.

BIPA: a database for protein-nucleic acid interaction in 3D structures.

Lee S, Blundell TL.

Bioinformatics. 2009 Jun 15;25(12):1559-60. doi: 10.1093/bioinformatics/btp243. Epub 2009 Apr 8.

11.

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures.

Popenda M, Blazewicz M, Szachniuk M, Adamiak RW.

Nucleic Acids Res. 2008 Jan;36(Database issue):D386-91. Epub 2007 Oct 5.

12.

PRince: a web server for structural and physicochemical analysis of protein-RNA interface.

Barik A, Mishra A, Bahadur RP.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W440-4. doi: 10.1093/nar/gks535. Epub 2012 Jun 11.

13.

PDTD: a web-accessible protein database for drug target identification.

Gao Z, Li H, Zhang H, Liu X, Kang L, Luo X, Zhu W, Chen K, Wang X, Jiang H.

BMC Bioinformatics. 2008 Feb 19;9:104. doi: 10.1186/1471-2105-9-104.

14.

A new residue-nucleotide propensity potential with structural information considered for discriminating protein-RNA docking decoys.

Li CH, Cao LB, Su JG, Yang YX, Wang CX.

Proteins. 2012 Jan;80(1):14-24. doi: 10.1002/prot.23117. Epub 2011 Sep 26.

PMID:
21953889
15.

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.

16.

Voronoia: analyzing packing in protein structures.

Rother K, Hildebrand PW, Goede A, Gruening B, Preissner R.

Nucleic Acids Res. 2009 Jan;37(Database issue):D393-5. doi: 10.1093/nar/gkn769. Epub 2008 Oct 23.

17.

Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure.

Lejeune D, Delsaux N, Charloteaux B, Thomas A, Brasseur R.

Proteins. 2005 Nov 1;61(2):258-71.

PMID:
16121397
18.

iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions.

Finn RD, Marshall M, Bateman A.

Bioinformatics. 2005 Feb 1;21(3):410-2. Epub 2004 Sep 7.

19.

Exploiting structural and topological information to improve prediction of RNA-protein binding sites.

Maetschke SR, Yuan Z.

BMC Bioinformatics. 2009 Oct 18;10:341. doi: 10.1186/1471-2105-10-341.

20.

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.

Petrov AI, Zirbel CL, Leontis NB.

RNA. 2013 Oct;19(10):1327-40. doi: 10.1261/rna.039438.113. Epub 2013 Aug 22.

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