PTM Related Resources

PTM : Phosphorylation        Type : Database

dbPPT
Resource Type : DB
Description :
As one of the most important and ubiquitous post-translational modifications (PTMs), protein phosphorylation regulates a broad spectrum of biological processes not only in humans but also in plants. The identification of site-specific phosphorylated substrates is fundamental for understanding the re ...
Taxonomy : Eukaryota, Plants
Visit : http://dbppt.biocuckoo.org/

Publication Information

Article : dbPPT: a comprehensive database of protein phosphorylation in plants.
Author : Han Cheng, Wankun Deng, Yongbo Wang, Jian Ren, Zexian Liu and Yu Xue
Years : 2014
PubMed : 25534750

dbPSP
Resource Type : DB
Description :
As one of the most important and ubiquitous post-translational modifications (PTMs), protein phosphorylation regulates a broad spectrum of biological processes not only in humans but also in plants. The identification of site-specific phosphorylated substrates is fundamental for understanding the re ...
Taxonomy : Archaea, Bacteria
Visit : http://dbpsp.biocuckoo.org/

Publication Information

Article : dbPSP: a curated database for protein phosphorylation sites in prokaryotes.
Author : Zhicheng Pan, Bangshan Wang, Ying Zhang, Yongbo Wang, Shahid Ullah, Ren Jian, Zexian Liu, and Yu Xue
Years : 2015
PubMed : 25841437

HPRD
Resource Type : DB
Description :
COMMERCIAL ENTITIES MAY NOT USE THIS SITE WITHOUT PRIOR LICENSING AUTHORIZATION. PLEASE SEND AN E-MAIL FOR FURTHER INFORMATION ABOUT LICENSING. The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, pos ...
Taxonomy : Eukaryota, Animals
Visit : http://www.hprd.org/

Publication Information

Article : Human Protein Reference Database--2009 update.
Author : T. S. Keshava Prasad, Renu Goel, Kumaran Kandasamy, Shivakumar Keerthikumar, Sameer Kumar, Suresh Mathivanan, Deepthi Telikicherla, Rajesh Raju, Beema Shafreen, Abhilash Venugopal, Lavanya Balakrishnan, Arivusudar Marimuthu, Sutopa Banerjee, Devi S. Somanathan, Aimy Sebastian, Sandhya Rani, Somak Ray, C. J. Harrys Kishore, Sashi Kanth, Mukhtar Ahmed, Manoj K. Kashyap, Riaz Mohmood, Y. L. Ramachandra, V. Krishna, B. Abdul Rahiman, Sujatha Mohan, Prathibha Ranganathan, Subhashri Ramabadran, Raghothama Chaerkady and Akhilesh Pandey
Years : 2009
PubMed : 18988627

LymPHOS
Resource Type : DB
Description :
Current proteomic technology is capable of producing huge amounts of analytical information, which is often difficult to manage in a comprehensive form. Curation, further annotation and public communication of proteomic data require the development of standard data formats and efficient, multimedia ...
Taxonomy : Eukaryota, Animals
Visit : http://www.lymphos.org/

Publication Information

Article : LymPHOS: design of a phosphosite database of primary human T cells.
Author : David Ovelleiro, Montserrat Carrascal, Vanessa Casas andJoaquin Abian
Years : 2009
PubMed : 19639593

MAPRes
Resource Type : DB
Description :
The new version of MAPRes is an extension of old version of MAPRes to mine association rules on the basis of bio-physical and bio-chemical properties of the amino acids. Several studies have been performed to analyse primary sequence of the amino acids but analyses performed on the bases of physic-c ...
Taxonomy : N/A
Visit : http://www.imsb.edu.pk/Database.htm

Publication Information

Article : Exploring the sequence context of phosphorylatable amino acids: the contribution of the upgraded MAPRes tool.
Author : Daniel C. Hoessli,Wajahat M. Qazi,Munir Ahmad, Abdul Rauf Shakoori,Nasir-ud-Din
Years : 2015
PubMed : 25258092

P3DB
Resource Type : DB
Description :
P(3)DB (http://www.p3db.org/) provides a resource of protein phosphorylation data from multiple plants. The database was initially constructed with a dataset from oilseed rape, including 14,670 nonredundant phosphorylation sites from 6382 substrate proteins, representing the largest collection of pl ...
Taxonomy : Eukaryota, Plants
Visit : http://www.p3db.org/

Publication Information

Article : P3DB: a plant protein phosphorylation database.
Author : Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen and Dong Xu
Years : 2009
PubMed : 18931372

PepCyber:P~PEP
Resource Type : DB
Description :
PepArray pro is a proteomics tool to provide PepArray Layout file that contains information about peptides, peptide IDs, and the array-location of the peptides to be synthesized on chip. The Layout file is required by the synthesis of an addressable peptide microarray. Peptide microarrays (PepArra ...
Taxonomy : Eukaryota, Animals
Visit : http://www.pepcyber.org/PPEP/copyright.php

Publication Information

Article : PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains.
Author : Wuming Gong, Dihan Zhou, Yongliang Ren, Yejun Wang, Zhixiang Zuo, Yanping Shen, Feifei Xiao, Qi Zhu, Ailing Hong, Xiaochuan Zhou, Xiaolian Gao and Tongbin Li
Years : 2008
PubMed : 18160410

PHOSIDA
Resource Type : DB
Description :
This database accompanies 'PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites', Florian Gnad, Shubin Ren, Juergen Cox, Jesper V Olsen, Boris Macek, Mario Oroshi, Matthias Mann (2007); Genome Biology. An update of the databas ...
Taxonomy : N/A
Visit : http://www.phosida.com/

Publication Information

Article : PHOSIDA 2011: the posttranslational modification database.
Author : Florian Gnad, Jeremy Gunawardena and Matthias Mann
Years : 2011
PubMed : 21081558

PhosPhAt
Resource Type : DB
Description :
Phosphorylation site database: The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt 3.0) contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. Specific information about the peptide pro ...
Taxonomy : Eukaryota, Plants
Visit : http://phosphat.uni-hohenheim.de/

Publication Information

Article : PhosPhAt goes kinases--searchable protein kinase target information in the plant phosphorylation site database PhosPhAt
Author : Monika Zulawski, Rostyslav Braginets and Waltraud X. Schulze
Years : 2013
PubMed : 23172287

Phospho.ELM
Resource Type : DB
Description :
Phospho.ELM is a database of experimentally verified phosphorylation sites in eukaryotic proteins. The current release (Version 9.0, September 2010) of Phospho.ELM contains 8,718 substrate proteins from different species covering more than 42,500 instances. Instances are fully linked to literature ...
Taxonomy : N/A
Visit : http://phospho.elm.eu.org/

Publication Information

Article : Phospho.ELM: a database of phosphorylation sites--update 2011
Author : Holger Dinkel, Claudia Chica, Allegra Via, Cathryn M. Gould, Lars J. Jensen, Toby J. Gibson1 and Francesca Diella
Years : 2011
PubMed : 21062810

Phospho3D
Resource Type : DB
Description :
Phospho3D is a database of three-dimensional structures of phosphorylation sites which stores information retrieved from the Phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database also collects the results of a large-scale structural ...
Taxonomy : N/A
Visit : http://www.phospho3d.org/

Publication Information

Article : Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites
Author : Andreas Zanzoni, Daniel Carbajo, Francesca Diella, Pier Federico Gherardini, Anna Tramontano, Manuela Helmer-Citterich and Allegra Via
Years : 2011
PubMed : 20965970

PhosphoGRID
Resource Type : DB
Description :
PhosphoGRID is an online database of experimentally verified in vivo protein phosphorylation sites in the model eukaryotic organism Saccharomyces cerevisisae. The database includes results from both high throughput (HTP) MS proteomics studies in addition to phosphosites identified in low throughput ...
Taxonomy : N/A
Visit : http://www.phosphogrid.org/

Publication Information

Article : The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update
Author : Ivan Sadowski, Bobby-Joe Breitkreutz, Chris Stark, Ting-Cheng Su, Matthew Dahabieh, Sheetal Raithatha, Wendy Bernhard, Rose Oughtred, Kara Dolinski, Kris Barreto and Mike Tyers
Years : 2013
PubMed : 23674503

PhosphoNET
Resource Type : DB
Description :
PhosphoNET is an open-access, online resource developed by Kinexus Bioinformatics Corporation to foster the study of cell signalling systems to advance biomedical research in academia and industry. PhosphoNET is the world’s largest repository of known and predicted information on human phosphorylati ...
Taxonomy : Eukaryota, Animals
Visit : http://www.phosphonet.ca/

Publication Information

Article : Prediction of 492 human protein kinase substrate specificities
Author : Javad Safaei, Ján Ma?uch, Arvind Gupta, Ladislav Stacho, Steven Pelech
Years : 2011
PubMed : 22165948

PhosphoPOINT
Resource Type : DB
Description :
MOTIVATION: To fully understand how a protein kinase regulates biological processes, it is imperative to first identify its substrate(s) and interacting protein(s). However, of the 518 known human serine/threonine/tyrosine kinases, 35% of these have known substrates, while 14% of the kinases have id ...
Taxonomy : Eukaryota, Animals
Visit : http://kinase.bioinformatics.tw/

Publication Information

Article : PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database.
Author : Chia-Ying Yang, Chao-Hui Chang, Ya-Ling Yu, Tsu-Chun Emma Lin, Sheng-An Lee, Chueh-Chuan Yen, Jinn-Moon Yang, Jin-Mei Lai, Yi-Ren Hong, Tzu-Ling Tseng, Kun-Mao Chao and Chi-Ying F. Huang
Years : 2008
PubMed : 18689816

PhospoPep
Resource Type : DB
Description :
PhospoPep version 2.0 is a project to support systems biology signaling research by providing interactive interrogation of MS-derived phosphorylation data from 4 different organisms. Currently there is data from the fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), ...
Taxonomy : N/A
Visit : http://www.phosphopep.org/

Publication Information

Article : Phosphoproteome resource for systems biology research
Author : Bernd Bodenmiller, Ruedi Aebersold
Years : 2011
PubMed : 21082442

PhosSNP
Resource Type : DB
Description :
As we are entering the age of "Personal Genomics" or "Personalized Medicine", it has been expected that the knowledge of human genetic polymorphisms and variations could provide a foundation for understanding differences in susceptibility to diseases and designing individualized therapeutic treatmen ...
Taxonomy : N/A
Visit : http://phossnp.biocuckoo.org/

Publication Information

Article : PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation
Author : Jian Ren, Chunhui Jiang, Xinjiao Gao, Zexian Liu, Zineng Yuan, Changjiang Jin, Longping Wen, Zhaolei Zhang, Yu Xue and Xuebiao Yao
Years : 2010
PubMed : 19995808

SubPhos
Resource Type : DB
Description :
Protein phosphorylation is the most common post-translational modification (PTM) regulating major cellular processes such as cell division, growth, and differentiation through highly dynamic and complex signaling pathways. However, the dynamic interplay of protein phosphorylation is not occurring ra ...
Taxonomy : Eukaryota, Animals
Visit : http://bioinfo.ncu.edu.cn/SubPhos.aspx

Publication Information

Article : Proteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity
Author : Xiang Chen, Shao-Ping Shi, Sheng-Bao Suo, Hao-Dong Xu and Jian-Ding Qiu
Years : 2015
PubMed : 25236462