Services
NetPhospan - 1.0
Prediction of phosphorylation using convolutional neural networks (CNNs).
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.
Predictions can be made for peptides of length 21.
Link to table (tab seperated) describing the training data Training data table
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
Usage instructions
1. Specify the input sequences
All the input sequences must be in one-letter amino acid code. The allowed alphabet (not case sensitive) is as follows:
All the other symbols will be converted to X before processing.
The server allows for input in either FASTA or PEPTIDE format.
Note that for Peptide input, all peptides MUST of equal length. Note also, that you must click the box Click if input is PEPTIDE format if the input is in peptide format.
The sequences can be input in the following two ways:
-
Paste a single sequence (just the amino acids) or a number of sequences in
FASTA
format or a list of peptides into the upper window of the main server page.
- Select a FASTA or PEPTIDE file on your local disk, either by typing the file name into the lower window or by browsing the disk.
Both ways can be employed at the same time: all the specified sequences will
be processed. However, there may be not more than 10 sequences
in total in one submission.
The sequences shorter than 15
or longer than 10000 amino acids will be ignored.
2. Customize your run
Use Method Selection to specify if you want to use the Pan-specific predictor or the Generic predictor. The Pan-specific method is trained with peptides and kinase sequences and predicts phosphorylation for the selected (or provided) kinases. The Generic method was trained only with peptide sequences, without information on the kinase side.
If the method selected was Pan-specific, select the kinase(s) you want to make predictions for from the scroll-down menu, or type in the kinase names separated by commas (without blank spaces).
If the kinase that you are looking for is not in the list, a full length protein kinase domain sequence can be submitted.
Select one option from Sort by score to have the output sorted by descending order.
Click the box save prediction to xls file to save the raw prediction output to an excel file. This file
will be available in the bottom of the results output file.
3. Submit the job
Click on the "Submit" button. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.
At any time during the wait you may enter your e-mail address and simply leave
the window. Your job will continue; you will be notified by e-mail when it has
terminated.
The e-mail message will contain the URL under which the results are
stored; they will remain on the server for 24 hours for you to collect them.
Output format
DESCRIPTION
OUTPUT EXAMPLE
# NetPhospan version 1.0 # Tmpdir made /scratch/netPhospanq4riRd # Input is in FSA format # Peptide length 21 ----------------------------------------------------------------------------------------------------- pos kin peptide Identity Pred Flag ----------------------------------------------------------------------------------------------------- 0 PKACA GEIYDALDMLTRENVALKVES TTBK2 0.028 0 0 PKACA TRENVALKVESAQQPKQVLKM TTBK2 0.192 0 0 PKACA QGRNLADLRRSQSRGTFTIST TTBK2 0.755 1 0 PKACA RNLADLRRSQSRGTFTISTTL TTBK2 0.847 1 0 PKACA ADLRRSQSRGTFTISTTLRLG TTBK2 0.602 1 0 PKACA LRRSQSRGTFTISTTLRLGRQ TTBK2 0.306 0 0 PKACA RSQSRGTFTISTTLRLGRQIL TTBK2 0.305 0 ----------------------------------------------------------------------------------------------------- Protein TTBK2. Kinase PKACA. Number of peptides 24 -----------------------------------------------------------------------------------------------------