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Results: 1 to 20 of 28

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]

PMID:
24830415
[PubMed - as supplied by publisher]
Free PMC Article
2.

Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends.

Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Myler PJ, Zilberstein D.

Mol Cell Proteomics. 2014 Jul;13(7):1787-99. doi: 10.1074/mcp.M114.037705. Epub 2014 Apr 16.

PMID:
24741111
[PubMed - in process]
3.

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.

PMID:
23758645
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Phosphoproteomic analysis of differentiating Leishmania parasites reveals a unique stage-specific phosphorylation motif.

Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Zilberstein D.

J Proteome Res. 2013 Jul 5;12(7):3405-12. doi: 10.1021/pr4002492. Epub 2013 Jun 11.

PMID:
23688256
[PubMed - indexed for MEDLINE]
5.

Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound.

Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Späth GF.

J Proteomics. 2013 Jun 28;86:97-104. doi: 10.1016/j.jprot.2013.05.002. Epub 2013 May 16.

PMID:
23684787
[PubMed - indexed for MEDLINE]
6.

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.

PMID:
23209685
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Experimental and computational methods for the analysis and modeling of signaling networks.

Gherardini PF, Helmer-Citterich M.

N Biotechnol. 2013 Mar 25;30(3):327-32. doi: 10.1016/j.nbt.2012.11.007. Epub 2012 Nov 16. Review.

PMID:
23165097
[PubMed - in process]
8.

Exploring the diversity of SPRY/B30.2-mediated interactions.

Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G.

Trends Biochem Sci. 2013 Jan;38(1):38-46. doi: 10.1016/j.tibs.2012.10.001. Epub 2012 Nov 17. Review.

PMID:
23164942
[PubMed - indexed for MEDLINE]
9.

Mapping the human phosphatome on growth pathways.

Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G.

Mol Syst Biol. 2012;8:603. doi: 10.1038/msb.2012.36.

PMID:
22893001
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
22888263
[PubMed]
Free PMC Article
11.

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.

PMID:
22536963
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

What has proteomics taught us about Leishmania development?

Tsigankov P, Gherardini PF, Helmer-Citterich M, Zilberstein D.

Parasitology. 2012 Aug;139(9):1146-57. doi: 10.1017/S0031182012000157. Epub 2012 Feb 28. Review.

PMID:
22369930
[PubMed - indexed for MEDLINE]
13.

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.

PMID:
22182631
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
21622655
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani.

Schmidt-Arras D, Leclercq O, Gherardini PF, Helmer-Citterich M, Faigle W, Loew D, Späth GF.

J Proteomics. 2011 Aug 24;74(9):1644-51. doi: 10.1016/j.jprot.2011.03.024. Epub 2011 Mar 26.

PMID:
21443974
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
20974634
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.

Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D268-71. doi: 10.1093/nar/gkq936. Epub 2010 Oct 21.

PMID:
20965970
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Identification of Leishmania-specific protein phosphorylation sites by LC-ESI-MS/MS and comparative genomics analyses.

Hem S, Gherardini PF, Osorio y Fortéa J, Hourdel V, Morales MA, Watanabe R, Pescher P, Kuzyk MA, Smith D, Borchers CH, Zilberstein D, Helmer-Citterich M, Namane A, Späth GF.

Proteomics. 2010 Nov;10(21):3868-83. doi: 10.1002/pmic.201000305.

PMID:
20960452
[PubMed - indexed for MEDLINE]
19.

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.

PMID:
20700534
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
20185567
[PubMed - indexed for MEDLINE]
Free PMC Article

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