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PhosK3D is a web server for identifying kinase-specific phosphorylation sites on protein sequences and three-dimensional structures. Due to the importance of protein phosphorylation in cellular control mechanism, version 1.0 and 2.0 of KinasePhos have been proposed for accurately identify the kinase-specific phosphorylation sites. With the high-throughput of mass spectrometry-based phospho-proteomics, the desire to comprehensively annotate the catalytic kinases for in vivo phosphorylation sites has motivated. Herein, a new web resource, PhosK3D, has been developed for performing a large-scale prediction of over 100 kinase-specific groups which contain sufficient number of experimental substrate sites. To identify phosphorylation sites on protein 3D structures, this work incorporated support vector machine (SVM) with the information of spatial amino acid composition and structural alphabet, which is a new feature to encode a 3D structure fragment of protein backbones into 23 structural alphabets. After the cross-validation evaluation, most of the kinase-specific models trained with the consideration of structural information outperform the models considering only the sequence information. Moreover, the independent testing set which is not included in the training set has demonstrated that the KinasePhos3D could provide a comparable performance to other popular tools.

 

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Case Study

P56LCK SH2 Domain Inhibitor Complex

 

Pyruvate Kinase from Saccharomyces Cerevisiae Complexed with FBP, PG, MN2+ and K+

●Figure. 3D structure.


 

Submission

 

 

Upload structure file from your computer(PDB format):     

or


Enter a PDB enty code (i.e.: 1A2X):   


Serine(S) Kinase:
CDK CK1 CK2 PIKK
MAPK PKA PKB PKC
PKG PLK STE20
Threonine(T) Kinase:
MAPK PKA PKC STE20
Tyrosine(Y) Kinase:
Abl EGFR FGFR InsR
Src Syk


Serine(S)/Threonine(T) Kinase => check all:

AMPKATMAurAAurB
AurBARKBRSKCAMK1
CAMK2CAMKKCDC2CDK7
CDKChaKCHK1CHK2
CK1CK2CLKDAPK
DDRDNAPKDYRKEph
ERKFRAPGEKGRK
GSKHIPKIKKIRAK
JNKKHSLKBMAP2K
MAP3KMAPKAPKMAPKMARK
MELKMLCKMNKMSK
MSNMSTNDRNEK
nmoNuaKp38p70
PAKAPAKBPAKPDHK
PDK1PHKPIMPKA
PKBPKCPKCPKC
PKCPKCPKDPKG
PKNPKRPLKQIK
RAFROCKRSKSGK
STKRSTKRTAF1TGFbR
TTBKTTKULKVRK
WNKYSK

Tyrosine(Y) Kinase => check all:

AblAckAxlBrk
BTKCskDYRKEGFR
EphERKFAKFer
FesFGFRFgrFms
FynHCKIGF1RInsR
ITKJakAKitLck
LYNMAP2KMAPKMet
PDGFRRetSrcSYK
TecTieTrkTXK
TYK2VEGFRWEEYES
ZAP70




 



Contact Us

 

Question & Comments:

Contact Prof. Tzong-Yi Lee.

 

Server Maintain:

Contact student Min-Gang Su.