NetPhospan 1.0 Server

Prediction of phosphorylation using convolutional neural networks (CNNs).

View the version history of this server. All previous versions are available online, for comparison and reference.

NetPhospan server predicts phophorylation from any human kinase of known sequence using convolutional neural networks (CNNs). The method is trained on more than 8,700 reported phosphorylation sites by 120 different human protein kinase from homo sapiens. Furthermore, the server admits custom kinases provided as full length sequences in FASTA format.

Version 1.0 has been trained using the method described in this paper

Predictions can be made for peptides of length 21.

Link to table (tab seperated) describing the training data Training data table

Instructions

Output format

Article abstract

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SUBMISSION

Hover the mouse cursor over the symbol for a short description of the options

Type of input Fasta Peptide

Paste a single sequence or several sequences in FASTA format into the field below:

or submit a file in FASTA format directly from your local disk:

Paste a single or several peptides in PEPTIDE format into the field below:

or submit a file in PEPTIDE format directly from your local disk:

Method Selection
Pan-specific method
Generic method

Select kinase group
AGC CAMK CK1 CMGC Other RGC STE TK TKL
Select Kinase (max 20 per submission) AKT1 AKT2 AKT3 BARK1 PKG1 PKG2 DMPK1 DMPK2 GPRK4 GPRK5 GPRK6 MAST3 MAST2 MRCKb MSK1 MSK2 NDR1 ROCK2 p70S6K p70S6Kb PKCh PDK1 MRCKa PKACa PKACb PKACg PKCa PKCb PKCd PKCe PKCg PKCi PKCt PKCz PRKX PKN1 PKN2 PRKY RHOK ROCK1 RSK1 RSK2 RSK3 MAST1 LATS1 LATS2 MASTL YANK3 RSKL2 BARK2 YANK2 SgK494 NDR2 PKN3 RSKL1 RSK4 SGK2 SGK3 GPRK7 YANK1 SGK1 CRIK MAST4 Trb1 BRSK2 CaMK1g AMPKa1 AMPKa2 CaMK1a CaMK2a CaMK2b CaMK2g CaMK4 VACAMKL CASK CHK1 CHK2 MARK3 DAPK1 DAPK2 MARK2 Trb2 NuaK1 PIM3 LKB1 MAPKAPK2 MAPKAPK3 MAPKAPK5 MARK1 smMLCK MNK1 MNK2 PHKg1 PHKg2 PIM1 PIM2 MELK PKD1 PSKH1 TTN Trio NIM1 STK33 TSSK3 NuaK2 TSSK2 PKD2 DRAK1 DRAK2 PKD3 SgK495 PASK QSK HUNK QIK MARK4 SSTK Trad TSSK4 caMLCK SPEG CaMK1d BRSK1 Obscn PSKH2 SIK SNRK CaMK1b skMLCK Trb3 CaMK2d TSSK1 SgK085 DAPK3 CK1a CK1d CK1e CK1g2 CK1g3 VRK1 VRK2 TTBK2 TTBK1 VRK3 CK1a2 CK1g1 CDK7 CDC2 CDK2 CDK3 CDK4 CDK5 CDK6 CDK8 CHED CLK1 CLK2 CLK3 DYRK1B DYRK2 DYRK4 Erk1 Erk2 Erk3 Erk4 GSK3A GSK3B HIPK1 JNK1 JNK2 JNK3 CDKL2 CDKL1 MAK DYRK1A NLK p38a PCTAIRE1 PCTAIRE2 PCTAIRE3 PFTAIRE1 CDK10 CDK9 PITSLRE HIPK3 PRP4 p38b p38g p38d SRPK1 SRPK2 CDKL5 Erk5 CDK11 PFTAIRE2 Erk7 CDKL4 CCRK CLK4 CRK7 DYRK3 HIPK2 ICK MOK MSSK1 CDKL3 HIPK4 Wnk2 AurC BUBR1 CDC7 CK2a1 CK2a2 PKR GAK IKKa IKKb IRE1 IKKe Fused MOS MYT1 NEK1 NEK2 NEK3 NEK4 PIK3R4 PEK PLK1 PLK3 PLK4 PLK2 TLK1 TLK2 TTK ULK1 ULK2 Wee1 AurB AurA BUB1 NEK6 NEK7 AAK1 ULK3 CLIK1L SCYL1 PINK1 ULK4 SgK493 PRPK SCYL3 NEK9 SCYL2 NEK8 NRBP1 CaMKK2 GCN2 CLIK1 HRI IRE2 MPSK1 Wnk1 SgK496 NRBP2 SgK071 Slob PBK TBK1 NEK5 NEK11 SgK069 Wnk4 SgK110 SgK196 Wnk3 SgK223 NEK10 SgK269 SBK SgK396 KIS TBCK Haspin CaMKK1 SgK307 BIKE SgK424 Wee1B RNAseL ANPa ANPb CYGD CYGF HSER GCK COT HPK1 KHS1 MAP2K1 MAP2K2 MAP2K5 MAP2K6 MAP3K1 MAP3K2 MAP3K3 MAP3K4 MAP3K5 MAP2K7 MAP2K3 MAP2K4 MST1 MST2 MST3 NIK PAK1 PAK2 PAK3 HGK SLK TAO2 YSK1 LOK KHS2 OSR1 PAK6 PAK4 MST4 STLK3 STLK5 STLK6 TAO3 TAO1 MAP3K6 PAK5 MAP3K8 MYO3B MYO3A MAP3K7 NRK MINK ABL1 ABL2 ACK ALK AXL BLK BRK BTK FMS CSK EGFR EphA1 EphA2 EphA3 EphA4 EphA5 EphA8 EphB1 EphB2 EphB3 EphB4 EphB6 FAK FER FES FGFR1 FGFR2 FGFR3 FGFR4 FGR FLT3 FLT1 FLT4 FYN HCK IGF1R INSR IRR ITK JAK1 JAK2 JAK3 KIT LCK LTK LYN MER MET MUSK PDGFRa PDGFRb RET RON ROR1 ROR2 ROS RYK SRC SYK TEC TIE2 TIE1 TNK1 TRKA TRKB TRKC TXK TYK2 TYRO3 YES ZAP70 DDR1 KDR DDR2 CCK4 LMR1 LMR2 LMR3 EphA7 BMX CTK FRK PYK2 SRM ErbB4 SuRTK106 EphA10 EphA6 ErbB3 ErbB2 ACTR2 ACTR2B ALK1 ALK2 BMPR1A ALK4 TGFbR1 BMPR1B ARAF BRAF DLK ILK IRAK1 IRAK2 IRAK3 KSR1 LIMK2 MISR2 MLK1 MLK2 IRAK4 RAF1 RIPK1 RIPK2 RIPK3 MLK3 TAK1 BMPR2 TESK1 TGFbR2 LZK ALK7 LIMK1 MLKL HH498 ZAK TESK2 ANKRD3 KSR2 SgK288 LRRK2 MLK4 LRRK1 or type Kinase gene name (e.g. AKT1) separated by commas (and no spaces). (Max 20 kinases per submission). 

For list of allowed kinase names click here List of Kinase gene names.

or paste a single full length kinase domain protein sequence in FASTA format into the field below:

or submit a file containing a full kinase domain protein sequence in FASTA format directly from your local disk:

Sort by predicted score 

Save predictions to XLS file 

Restrictions:
At most 5000 sequences per submission; each sequence not more than 20,000 amino acids and not less than 8 amino acids. Max 20 kinase domains per submission.

Confidentiality:
The sequences are kept confidential and will be deleted after processing.

CITATIONS

For publication of results, please cite:

A generic Deep Convolutional Neural Network framework for prediction of Receptor-ligand Interactions. NetPhosPan; Application to Kinase Phosphorylation prediction.
Emilio Fenoy, Jose M. G. Izarzugaza, Vanessa Jurtz, Søren Brunak and Morten Nielsen.
Bioinformatics (2018).
Full text  

DATA RESOURCES

Kinase domain sequences were obtained from

• KinBase database. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science. 2002 Dec 6;298(5600):1912-34.

Phosphorylated sequences were obtained from

• Phospho.ELM database. Craveur P, Rebehmed J, de Brevern AG; PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins. Database (Oxford) 2014; 2014 bau041. doi: 10.1093/database/bau041.
• PhosphositePlus database. Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E; PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res 2015; 43 (D1): D512-D520. doi: 10.1093/nar/gku1267

PORTABLE VERSION

Would you prefer to run NetPhospan at your own site? NetPhospan v. 1.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. There is a download page for academic users; other users are requested to contact CBS Software Package Manager at software@cbs.dtu.dk.

GETTING HELP