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Protocols

GPS specifications

Information


Unique identifier OMICS_05929
Name GPS
Alternative name Group-based Prediction System
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data A primary sequence or multiple proteins sequences.
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 3.0
Stability Stable
Maintained Yes

Subtool


  • DOG

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Jian Ren
  • person_outline Yu Xue
  • person_outline Yongbo Wang

Additional information


http://gps.biocuckoo.org/userguide.php

Information


Unique identifier OMICS_05929
Name GPS
Alternative name Group-based Prediction System
Interface Web user interface
Restrictions to use None
Input data A primary sequence or multiple proteins sequences.
Input format FASTA
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • DOG

Documentation


Maintainers


  • person_outline Jian Ren
  • person_outline Yu Xue
  • person_outline Yongbo Wang

Additional information


http://gps.biocuckoo.org/userguide.php

Publications for Group-based Prediction System

GPS citations

 (37)
library_books

Casein kinase II phosphorylation of cyclin F at serine 621 regulates the Lys48 ubiquitylation E3 ligase activity of the SCF(cyclin F) complex

2017
Open Biol
PMCID: 5666078
PMID: 29021214
DOI: 10.1098/rsob.170058

[…] horylated by the canonical series of cyclin-dependent kinases and must be modified by kinases that are independent of cell-cycle regulation to ultimately regulate the SCF(cyclin F) complex. Using the group-based prediction system (GPS) [], numerous MAPKs, CDKs and NEKs were identified as potential kinases that could phosphorylate the newly identified phosphosites in cyclin F ().Casein kinase II (C […]

library_books

Phosphorylation of FE65 at threonine 579 by GSK3β stimulates amyloid precursor protein processing

2017
Sci Rep
PMCID: 5622059
PMID: 28963516
DOI: 10.1038/s41598-017-12334-2

[…] inding to APP, we speculated that FE65 T579 phosphorylation may alter APP metabolism, and attempted to identify the responsible kinase(s). By using various in silico kinase prediction tools including Group-based Prediction System Version 3.0 and NetworKIN 3.0,, glycogen synthase kinase 3β (GSK3β) was predicted to be a putative FE65 T579 kinase. In this study, we showed that FE65 is phosphorylated […]

library_books

eIF4B phosphorylation at Ser504 links synaptic activity with protein translation in physiology and pathology

2017
Sci Rep
PMCID: 5585320
PMID: 28874824
DOI: 10.1038/s41598-017-11096-1

[…] entify the kinases mediating phosphorylation of eIF4B at Ser504, we searched for kinase-specific phosphorylation motifs encompassing this residue with the bioinformatics tools PhosphoMotif Finder and Group-based Prediction System (GPS 2.1 software). We found that Ser504 is located in putative consensus sequences for the following kinases: MAPKs, cyclin-dependent kinase 5 (CDK5), casein kinase (CK) […]

library_books

CDK6 protects epithelial ovarian cancer from platinum‐induced death via FOXO3 regulation

2017
PMCID: 5623833
PMID: 28778953
DOI: 10.15252/emmm.201607012

[…] Addgene: http://www.addgene.org/ Addgene is a non‐profit plasmid repository dedicated to helping scientists around the world share high‐quality plasmids.GPS3.0 (Group‐based Prediction System, version 3.0): http://gps.biocuckoo.org/ GPS3.0 is a prediction software available online that could predict kinase‐specific phosphorylation sites for 408 human PKs in hi […]

library_books

Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera)

2017
Sci Rep
PMCID: 5434016
PMID: 28512345
DOI: 10.1038/s41598-017-02192-3

[…] ences of A. mellifera proteome (version 3.2) downloaded from Bee Base (www.beebase.org) by BLAST search. Finally, we obtained 906,294 non-redundant PPIs in 8,336 proteins of A. mellifera. Thereafter, group-based prediction system (GPS) software package, was used to predict the kinase-specific phosphosites. As the developed GPS tool was mainly used for prediction of kinase-specific phosphosites in […]

library_books

Smek promotes corticogenesis through regulating Mbd3’s stability and Mbd3/NuRD complex recruitment to genes associated with neurogenesis

2017
PLoS Biol
PMCID: 5414985
PMID: 28467410
DOI: 10.1371/journal.pbio.2001220

[…] ase []. To further investigate the involvement of PKCλ/ι in the molecular mechanism for Mbd3 protein stability, we performed prediction of putative kinases for phosphorylation of Mbd3 protein by GPS (group-based prediction system) software 3.0 (http://gps.biocuckoo.org/). (). Interestingly, we predicted PKCλ/ι as putative kinases for Mbd3 phosphorylation. Although it still remains unclear how Smek […]

Citations

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GPS institution(s)
Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, Hefei, China; School of Life Sciences, Sun Yat-sen University (SYSU), Guangzhou, China
GPS funding source(s)
Supported by grants from the National Basic Research Program (973 project) (2010CB945400, 2007CB94 7401), National Natural Science Foundation of China (90919001, 30700138, 30900835, 30830036, 31071154), and Chinese Academy of Sciences (INFO-115-C01-SDB4-36).

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