Publications
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Experimental and computational methods for the analysis and modeling of signaling networks.
Gherardini PF,
Helmer-Citterich M.
N Biotechnol.
2013;
30
(3):
327-32
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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;
38
(1):
38-46
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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
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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:
13 Suppl 4
S17
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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
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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
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What has proteomics taught us about Leishmania development?
Tsigankov P,
Gherardini PF, Helmer-Citterich M, Zilberstein D.
Parasitology.
2012;
139
(9):
1146-57
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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;
74
(9):
1644-51
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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:
12
614
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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;
39
(Web Server issue):
W278-82
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Phosphate binding sites identification in protein structures.
Parca L,
Gherardini PF, Helmer-Citterich M, Ausiello G.
Nucleic Acids Res.
2011;
39
(4):
1231-42
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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;
39
(Database issue):
D268-71
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Identification from chest x-rays: reliability of bone density patterns of the humerus.
Ciaffi R,
De Angelis D, Gherardini PF, Arcudi G, Nessi R, Cornalba GP, Grandi M, Cattaneo C.
J Forensic Sci.
2010;
55
(2):
478-81
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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;
10
(21):
3868-83
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Modular architecture of nucleotide-binding pockets.
Gherardini PF,
Ausiello G, Russell RB, Helmer-Citterich M.
Nucleic Acids Res.
2010;
38
(11):
3809-16
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Superpose3D: a local structural comparison program that allows for user-defined structure representations.
Gherardini PF,
Ausiello G, Helmer-Citterich M.
PLoS One.
2010;
5
(8):
e11988
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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:
10
182
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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:
9 Suppl 2
S2
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Structure-based function prediction: approaches and applications.
Gherardini PF,
Helmer-Citterich M.
Brief Funct Genomic Proteomic.
2008;
7
(4):
291-302
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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;
35
(Web Server issue):
W416-9
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Convergent evolution of enzyme active sites is not a rare phenomenon.
Gherardini PF,
Wass MN, Helmer-Citterich M, Sternberg MJ.
J Mol Biol.
2007;
372
(3):
817-45
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False occurrences of functional motifs in protein sequences highlight evolutionary constraints.
Via A,
Gherardini PF, Ferraro E, Ausiello G, Scalia Tomba G, Helmer-Citterich M.
BMC Bioinformatics.
2007:
8
68
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Phospho3D: a database of three-dimensional structures of protein phosphorylation sites.
Zanzoni A,
Ausiello G, Via A, Gherardini PF, Helmer-Citterich M.
Nucleic Acids Res.
2007;
35
(Database issue):
D229-31
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