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Results: 1 to 20 of 33

1.

A proteome-wide Domain-centric Perspective on Protein Phosphorylation.

Palmeri A, Ausiello G, Ferre F, Helmer-Citterich M, Gherardini PF.

Mol Cell Proteomics. 2014 May 15. pii: mcp.M114.039990. [Epub ahead of print]

2.

A novel approach to represent and compare RNA secondary structures.

Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M.

Nucleic Acids Res. 2014 Jun;42(10):6146-57. doi: 10.1093/nar/gku283. Epub 2014 Apr 21.

3.

DBATE: database of alternative transcripts expression.

Bianchi V, Colantoni A, Calderone A, Ausiello G, Ferrè F, Helmer-Citterich M.

Database (Oxford). 2013 Jul 9;2013:bat050. doi: 10.1093/database/bat050. Print 2013.

4.

Alternative splicing tends to avoid partial removals of protein-protein interaction sites.

Colantoni A, Bianchi V, Gherardini PF, Tomba GS, Ausiello G, Helmer-Citterich M, Ferrè F.

BMC Genomics. 2013 Jun 7;14:379. doi: 10.1186/1471-2164-14-379.

5.

webPDBinder: a server for the identification of ligand binding sites on protein structures.

Bianchi V, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W308-13. doi: 10.1093/nar/gkt457. Epub 2013 Jun 3.

6.

Nucleos: a web server for the identification of nucleotide-binding sites in protein structures.

Parca L, Ferré F, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W281-5. doi: 10.1093/nar/gkt390. Epub 2013 May 22.

7.

Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity.

Parca L, Gherardini PF, Truglio M, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G.

PLoS One. 2012;7(11):e50240. doi: 10.1371/journal.pone.0050240. Epub 2012 Nov 27.

8.

B-Pred, a structure based B-cell epitopes prediction server.

Giacò L, Amicosante M, Fraziano M, Gherardini PF, Ausiello G, Helmer-Citterich M, Colizzi V, Cabibbo A.

Adv Appl Bioinform Chem. 2012;5:11-21. doi: 10.2147/AABC.S30620. Epub 2012 Jul 25.

9.

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.

Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S17. doi: 10.1186/1471-2105-13-S4-S17.

10.

PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae.

Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Späth GF, Zilberstein D, Helmer-Citterich M.

BMC Genomics. 2011 Dec 19;12:614. doi: 10.1186/1471-2164-12-614.

11.

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.

Parca L, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W278-82. doi: 10.1093/nar/gkr389. Epub 2011 May 26.

12.

Phosphate binding sites identification in protein structures.

Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G.

Nucleic Acids Res. 2011 Mar;39(4):1231-42. doi: 10.1093/nar/gkq987. Epub 2010 Oct 24.

13.

Superpose3D: a local structural comparison program that allows for user-defined structure representations.

Gherardini PF, Ausiello G, Helmer-Citterich M.

PLoS One. 2010 Aug 5;5(8):e11988. doi: 10.1371/journal.pone.0011988.

14.

Modular architecture of nucleotide-binding pockets.

Gherardini PF, Ausiello G, Russell RB, Helmer-Citterich M.

Nucleic Acids Res. 2010 Jun;38(11):3809-16. doi: 10.1093/nar/gkq090. Epub 2010 Feb 25.

15.

Structural motifs recurring in different folds recognize the same ligand fragments.

Ausiello G, Gherardini PF, Gatti E, Incani O, Helmer-Citterich M.

BMC Bioinformatics. 2009 Jun 15;10:182. doi: 10.1186/1471-2105-10-182.

16.

Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information.

Ferrè F, Via A, Ausiello G, Brannetti B, Zanzoni A, Helmer-Citterich M.

Comp Funct Genomics. 2003;4(4):416-9. doi: 10.1002/cfg.304.

17.

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.

Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M.

BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S2. doi: 10.1186/1471-2105-9-S2-S2.

18.

3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.

Via A, Peluso D, Gherardini PF, de Rinaldis E, Colombo T, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W416-9. Epub 2007 May 8.

19.

SH3-Hunter: discovery of SH3 domain interaction sites in proteins.

Ferraro E, Peluso D, Via A, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W451-4. Epub 2007 May 7.

20.

Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites.

Ausiello G, Peluso D, Via A, Helmer-Citterich M.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S24.

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