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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 in publications

 (5)
PMCID: 4139591
PMID: 25056123
DOI: 10.1007/s00894-014-2357-7

[…] 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 […]

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

[…] 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 […]

PMCID: 3542066
PMID: 23326221
DOI: 10.1371/journal.pcbi.1002842

[…] 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, […]

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

[…] 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 […]

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

[…] () 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 […]


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

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