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netphorest.info

NetPhorest 2.1

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.

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Linding Lab

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Rune Linding

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Rune Linding

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li●●●●●@lindinglab.org

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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.
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NetPhorest 2.1 | netphorest.info Reviews

https://netphorest.info

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.

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netphorest.info netphorest.info
1

NetPhorest 2.0

http://www.netphorest.info/index_ht.shtml

Select the sequence database:. Human - Ensembl 74. Human - Ensembl 73. Human - Ensembl 72. Human - Ensembl 71. Human - Ensembl 70. Human - Ensembl 69. Human - Ensembl 68. Human - STRING 9.0. Human - Uniprot 2013/12. Human - Uniprot 2013/01 (Maxquant). Human - NCBI 62. Yeast - Ensembl 74. Yeast - Ensembl 73. Yeast - Ensembl 72. Yeast - Ensembl 71. Yeast - Ensembl 70. Yeast - Ensembl 69. Yeast - Ensembl 68. Yeast - Uniprot 2013/12. Yeast - NCBI 62. Put modified sites below in the format:.

2

NetPhorest 2.0

http://www.netphorest.info/download.shtml

Here you can download the precomputed data for all available kinase predictors against ENSEMBL version 59 on known phosphorylation sites from the KinomeXplorer-DB. Select the kinases and/or the substrates of interest to filter and click on show result. To select multiple entries, hold the following buttons dependent on your operating system:. Windows and Linux: hold the control button to select multiple. Mac OS X: hold the command button to select multiple. NetworKIN3.0 release.zip.

3

NetPhorest 2.0

http://www.netphorest.info/help.shtml

Both algorithms work on the same input data, and you can switch at any point of the workflow between the different algorithms. Using KinomeXplorer on mouse. KinomeXplorer was trained on human and yeast data, and it is possible to use KinomeXplorer on their neighbour species, such as mouse. There are many studies that employed NetworKIN in species other than human and yeast, from which you can get some idea. For the analysis of high-throughput experiments (more than 100 sites), please refer to the high-th...

4

NetPhorest 2.0

http://www.netphorest.info/index.shtml

Paste sequences (FASTA format) or protein names (one per line) below. Example: #1. For protein names, HGNC symbol is recommended.). In case you have more than 100 sequences, please consider using the high throughput workflow. 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. C) 2005-2013 Rune Linding and Lars Juhl Jensen.

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elm.eu.org elm.eu.org

ELM - Help

http://elm.eu.org/help.html

The Eukaryotic Linear Motif resource for. Functional Sites in Proteins. What methods are used for detecting functional sites? Currently, patterns written as regular expressions. Why are the ELM predictions not scored? Since a regular expression either matches or does not match a string (or a protein subsequence), in its nature the score would be 1 or 0. What does the ELM instance mapper do? Uses PHI-BLAST to map ELM predictions of a query sequence to known annotated ELM instances. The basis for the m...

elm.eu.org elm.eu.org

ELM - Help

http://elm.eu.org/infos/help.html

The Eukaryotic Linear Motif resource for. Functional Sites in Proteins. What methods are used for detecting functional sites? Currently, patterns written as regular expressions. Why are the ELM predictions not scored? Since a regular expression either matches or does not match a string (or a protein subsequence), in its nature the score would be 1 or 0. What does the ELM instance mapper do? Uses PHI-BLAST to map ELM predictions of a query sequence to known annotated ELM instances. The basis for the m...

rekinect.info rekinect.info

ReKINect FAQ

http://www.rekinect.info/FAQ

ReKINect - Frequently Asked Questions. In a nutshell, what does ReKINect do? ReKINect is a computational framework that predicts the likely functionality of mutations. What do you mean with "likely functionality"? Can you be more specific? Ok, so what type of functional residues are currently been used? We are currently mapping onto 3 different types of functional residues:. A - Essential residues in protein domains (Kinase and SH2 domains). C - Phosphorylation sites in any protein. Every single amino-ac...

cbs.dtu.dk cbs.dtu.dk

CBS Prediction Servers

http://www.cbs.dtu.dk/services

This page is the main entry to the on-line prediction services at CBS. All the servers are available as interactive input forms. In order to view the full documentation and use a server click on the appropriate link in the list below. The access to all the servers is free and unlimited for all academic users. For other users the access is also free but limited (see the details. Of the access policy). Tab above to download software. Whole genome visualization and analysis. Gene finding and splice sites.

phospho.elm.eu.org phospho.elm.eu.org

Phospho.ELM Links

http://phospho.elm.eu.org/links.html

A database of S/T/Y phosphorylation sites. Phospho.ELM related links. DISPHOS computationally predicts serine, threonine and tyrosine phosphorylation sites in proteins. Resource for prediction functional sites in eukaryotic proteins. Group-based phosphorylation scoring methods. Is an atlas of consensus sequence motifs for kinases and phosphorylation-dependent binding domains. Prediction of Ser, Thr and Tyr phosphorylation sites using neural network. Systematic discovery of in vivo phosphorylation networks.

dynactome.mshri.on.ca dynactome.mshri.on.ca

The Pawson Lab - Home

http://dynactome.mshri.on.ca/index.php

SELPHI: correlation-based identification of kinase-associated networks. SELPHI: correlation-based identification of kinase-associated networks. People and Contact Info. Wednesday, 11 September 2013. Tony Pawson about science. Tony Pawson's Kyoto Prize Commemorative Lecture in Kyoto Japan. Last Updated ( Monday, 23 June 2014 ). SELPHI: correlation-based identification of kinase-associated networks. Written by Karen Colwill. Wednesday, 06 May 2015. Last Updated ( Friday, 05 June 2015 ). Homology 2 domain c...

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NetPhorest 2.1

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.

netphorest.science netphorest.science

NetPhorest 2.0

Paste sequences (FASTA format) or protein names (one per line) below. Example: #1. For protein names, HGNC symbol is recommended.). In case you have more than 100 sequences, please consider using the high throughput workflow. 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. C) 2005-2013 Rune Linding and Lars Juhl Jensen.

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