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Phos3D specifications

Information


Unique identifier OMICS_05938
Name Phos3D
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Phos3D

Phos3D citations

 (5)
library_books

Evidence supporting the existence of a NUPR1 like family of helix loop helix chromatin proteins related to, yet distinct from, AT hook containing HMG proteins

2014
J Mol Model
PMCID: 4139591
PMID: 25056123
DOI: 10.1007/s00894-014-2357-7

[…] phorylation were NetPhosk 1.0 and 2.0 [], Kinasephos 2.0 [], DIPHOS [], PhosphoSVM [], Scansite [], Musite [], PPSP [], and GPS 2.0 []. Additionally, 3D phosphorylation prediction was performed using Phos3D []. Acetylation sites were predicted using PAIL [], PREDMOD [], ASEB [], PLMLA [], PSKAcePred [], BRABSB-PHKA [], LysAcet [], and EnsemblePail []. Methylation sites were predicted using PMeS [] […]

library_books

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

2013
BMC Bioinformatics
PMCID: 3853090
PMID: 24564522
DOI: 10.1186/1471-2105-14-S16-S2

[…] ronment 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 motifs from 750 experimentally verified phosphorylation sites with 3D structures available in Protein Data Back (PDB) [] and applied them to implement a web server […]

library_books

Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins

2013
PLoS Comput Biol
PMCID: 3542066
PMID: 23326221
DOI: 10.1371/journal.pcbi.1002842

[…] ural information , combining data on linear motifs and structural properties , and development of software tools that use three-dimensional data for the prediction of phosphorylation sites (DISPHOS , Phos3D ). Large-scale studies of the structural characteristics of phosphorylation sites have focused on solvent exposure, local and global structure, amino acid context of the spatial surrounding, an […]

library_books

The viral transactivator HBx protein exhibits a high potential for regulation via phosphorylation through an evolutionarily conserved mechanism

2012
PMCID: 3533737
PMID: 23079056
DOI: 10.1186/1750-9378-7-27

[…] tein corresponding to clone isolate 4.5 as a reference.To analyze the phosphorylation potential of the HBx protein, we utilized several servers on the web such as NetPhos 2.0, DISPHOS 1.3, PPRED, and Phos3D [-]. These are neural networks-based programs that predict potential sites of serine, threonine, and tyrosine phosphorylation in polypeptides (Table‚ÄČ). The minimum threshold value used to predi […]

library_books

Virtual Interactomics of Proteins from Biochemical Standpoint

2012
PMCID: 3423939
PMID: 22928109
DOI: 10.1155/2012/976385

[…] s () to simulate interactions of 25 antibodies and P-glycoprotein, respectively. Frequent subset accuracies of higher values than the gold standard value of 0.80 were observed during runs of programs Phos3D, KinasePhos 2.0 (), ElliPro () and CBTOBE mentioned above (chapter 3; []), and two docking tools Glide XP and Gold (; []). Comparable AUC values then concerned RANKPEP (), BEOracle mentioned ab […]

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Phos3D institution(s)
Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany

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