NetPhorest 2.1 Update
We are happy to announce the release of NetPhorest 2.1, which fixes two major bugs that resulted in arbitrary scores from neural network predictors on SH2 domain, and partially arbitrary scores from neural networks on other domains. PSSM/scansite predictors remain unchanged.
Both web and command line versions were affected. We recommend repeating any analysis performed before May XX, 2017.
Learn more and download the updated binaries on the download page.
Here you can download the precomputed data for all available kinase predictors against ENSEMBL version 59 on known phosphorylation sites from the KinomeXplorer-DB.
Here are the changes to the algorihtms since the 2014 publication.
- NetPhorest 2.1
- Fix: SH2 neural network predictors were registered incorrectly and the scores were fully arbitrary (determined by the compiler).
- Fix: neural networks for all domains were registered incorrectly if they had no hidden layers, resulting in a shift of the weights.
Neural network scores are calculated as an average of 5-12 neural networks with mixed architectures. Approx. 15% of all networks have no hidden layers and produced arbitrary predictions (determined by the compiler). Nearly all nn predictors are affected to various degrees, except the following which had hidden layers for all neural networks:
KIN_CaMKIV, KIN_CaMKI_group, KIN_FLT3_CSF1R_Kit_PDGFR_group, KIN_IKKalpha_IKKbeta_group, KIN_KDR_FLT1_group, KIN_Met_group, KIN_PKC_group, KIN_ROCK_group, KIN_Syk_group, KIN_TTK, PTP_PTPN13, 1433_any_group.
PSSM (scansite) scores are not affected by this bug.
- Fix: possible buffer overflow with very long fasta names.
- The yeast release now behaves like the human: no prior filtering, and skips sites with unsupported amino acids.
- The NetPhorest binary now stops with an error message if it finds non-ASCII characters in the protein sequence.
We release all our data and source code. However, it should be noted that commercial entities can obtain a separate license that allow them to derive or use NetPhorest for commercial purposes. These entitites should contact the authors directly.
If you use any of the data from this web site please cite this article: Horn et al., KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods 2014 Jun;11(6):603–4
NetworKIN3.0_release.zip (This file contains source code and data files to run NetworKIN. Please refer to README.txt for more detailed instruction.)
NetPhorest_human_2.1.zip (This file contains source code to compile and run NetPhorest (human). Please refer to README.txt for more detailed instruction.)
NetPhorest_yeast_2.1.zip (This file contains source code to compile and run NetPhorest (yeast). Please refer to README.txt for more detailed instruction.)