Phospho3D statistics

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Phospho3D specifications


Unique identifier OMICS_03038
Name Phospho3D
Alternative name Phospho3D 2.0
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes




  • person_outline Manuela Helmer-Citterich
  • person_outline Andreas Zanzoni
  • person_outline Allegra Via

Additional information The downloadable complete dataset is available on request.

Publications for Phospho3D

Phospho3D citations


PredPhos: an ensemble framework for structure based prediction of phosphorylation sites

PMCID: 4943517
PMID: 27437197
DOI: 10.1186/s40709-016-0042-y

[…] n, mouse, fly, worm and yeast proteins. Also, PHOSIDA provides a wide range of analysis tools. Under the demand for analyzing the structural features of experimentally verified phosphorylation sites, Phospho3D [] was launched for storing information retrieved from Phospho.ELM and was enriched with structural information and annotation at the residue level.Given a long list of candidate phosphoryla […]


RegPhos 2.0: an updated resource to explore protein kinase–substrate phosphorylation networks in mammals

PMCID: 3999940
PMID: 24771658
DOI: 10.1093/database/bau034

[…] ), PHOSIDA () and PhosPhAt (). Additionally, the PhosphoGRID () is a new database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. The Phospho3D () is a database containing 3D structures of phosphorylation sites. The PhosphoPOINT () provides a robust annotation for kinases, downstream substrates and their interacting phosphoproteins, […]


Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase specific phosphorylation sites on protein three dimensional structures

BMC Bioinformatics
PMCID: 3853090
PMID: 24564522
DOI: 10.1186/1471-2105-14-S16-S2

[…] applied the structure-based information for improving the prediction of phosphorylation sites in proteins. With an increasing interest in the structural environment of protein phosphorylation sites, Phospho3D database [,] was proposed for characterizing the structural properties of phosphorylation sites on three-dimensional (3D) structures. Additionally, Phos3D [] has extracted 3D-signature motif […]


Charge environments around phosphorylation sites in proteins

BMC Struct Biol
PMCID: 2291461
PMID: 18366741
DOI: 10.1186/1472-6807-8-19

[…] enhance prediction accuracy for phosphorylation sites []. A database of 3D structures of protein phosphorylation sites has been developed, including structural annotation of the Phospho.ELM database (Phospho3D []). It has been noticed that the amino acid sequence properties around phosphorylation sites are similar to those of intrinsically disordered protein regions, and this information used to c […]


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Phospho3D institution(s)
Institute for Research in Biomedicine, Joint IRB-BSC program in Computational Biology, Barcelona, Spain; Biocomputing group, Department of Biochemical Sciences ‘A. Rossi Fanelli’, Sapienza University of Rome, Rome, Italy; European Molecular Biology Laboratory, Heidelberg; Biobyte solutions GmbH, Heidelberg, Germany; Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Italy
Phospho3D funding source(s)
Supported by Istituto Pasteur— Fondazione Cenci Bolognetti, Roma; the 7th EC Framework Programme LEISHDRUG project [grant number 223414]; and a ‘Juan de la Cierva’ fellowship.

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