PTM Related Resources

PTM : Phosphorylation        Type : Tool

AMS
Resource Type : Tool
Description :
We present here the 2011 update of the AutoMotif Service (AMS 4.0) that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The selection of experimentally confirmed modifications is acquired from the latest UniProt ...
Taxonomy : N/A
Visit : https://code.google.com/p/automotifserver/

Publication Information

Article : AMS 4.0: consensus prediction of post-translational modifications in protein sequences.
Author : Dariusz Plewczynski, Subhadip Basu, Indrajit Saha
Years : 2012
PubMed : 22555647

CKSAAP_PhSite
Resource Type : Tool
Description :
As one of the most widespread protein post-translational modifications, phosphorylation is involved in many biological processes such as cell cycle, apoptosis. Identification of phosphorylated substrates and their corresponding sites will facilitate the understanding of the molecular mechanism of ph ...
Taxonomy : N/A
Visit : http://59.73.198.144/cksaap_phsite/

Publication Information

Article : Prediction of protein phosphorylation sites by using the composition of k-spaced amino acid pairs.
Author : Xiaowei Zhao, Wenyi Zhang, Xin Xu, Zhiqiang Ma , Minghao Yin
Years : 2012
PubMed : 23110047

CRPhos
Resource Type : Tool
Description :
Welcome to the pTools webserver. This website is a joint development by the Centre for Proteome Analysis and the Intelligent Systems Lab, at the University of Antwerp. Here we present in-house developed tools for protein and proteome (data) analysis. Downloadable codes is shared here whenever a proj ...
Taxonomy : N/A
Visit : http://www.ptools.ua.ac.be/CRPhos

Publication Information

Article : Prediction of kinase-specific phosphorylation sites using conditional random fields.
Author : Thanh Hai Dang, Koenraad Van Leemput, Alain Verschoren and Kris Laukens
Years : 2008
PubMed : 18940828

DAPPLE
Resource Type : Tool
Description :
DAPPLE represents an alternative method (to machine-learning approaches) to predicting phosphorylation sites in an organism of interest. It is a pipeline involving BLAST searches that uses experimentally-determined phosphorylation sites in one organism (or several organisms) to predict phosphorylati ...
Taxonomy : N/A
Visit : http://saphire.usask.ca/saphire/dapple/index.html

Publication Information

Article : APPLE: a pipeline for the homology-based prediction of phosphorylation sites.
Author : Brett Trost, Ryan Arsenault, Philip Griebel, Scott Napper and Anthony Kusalik
Years : 2013
PubMed : 23658419

DISPHOS
Resource Type : Tool
Description :
DISPHOS computationally predicts serine, threonine and tyrosine phosphorylation sites in proteins. The new version of the predictor (DISPHOS 1.3) was trained on over 2000 non-redundant experimentally confirmed protein phosphorylation sites (1,079 Serine sites, 666 Threonine sites, and 375 Tyrosine s ...
Taxonomy : N/A
Visit : http://www.dabi.temple.edu/disphos/

Publication Information

Article : The importance of intrinsic disorder for protein phosphorylation.
Author : Lilia M. Iakoucheva, Predrag Radivojac, Celeste J. Brown, Timothy R. O’Connor, Jason G. Sikes, Zoran Obradovic and A. Keith Dunker
Years : 2004
PubMed : 14960716

GPS
Resource Type : Tool
Description :
Protein phosphorylation is the most ubiquitous post-translational modification (PTM), and plays important roles in most of biological processes. Identification of site-specific phosphorylated substrates is fundamental for understanding the molecular mechanisms of phosphorylation. Besides experimenta ...
Taxonomy : N/A
Visit : http://gps.biocuckoo.org/

Publication Information

Article : GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection.
Author : Yu Xue, Zexian Liu, Jun Cao, Qian Ma, Xinjiao Gao, Qingqi Wang, Changjiang Jin, Yanhong Zhou, Longping Wen and Jian Ren
Years : 2011
PubMed : 21062758

HMMpTM
Resource Type : Tool
Description :
During the last decades a large number of computational methods have been developed for predicting transmembrane protein structure and topology. Current predictors rely on two topogenic signals in the protein sequence: the distribution of positively charged residues in extra-membrane loops and the e ...
Taxonomy : N/A
Visit : http://aias.biol.uoa.gr/HMMpTM/

Publication Information

Article : HMMpTM: improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction.
Author : Georgios N. Tsaousisa, Pantelis G. Bagosb, Stavros J. Hamodrakasa
Years : 2014
PubMed : 24225132

KinasePhos
Resource Type : Tool
Description :
Protein phosphorylation is an important reversible mechanism in post-translational modifications of proteins, and it affects a lot of kinds of essential cellular processes. Due to the importance of protein phosphorylation in cellular control, there are many schemes and models to predict the catalyti ...
Taxonomy : N/A
Visit : http://kinasephos2.mbc.nctu.edu.tw/

Publication Information

Article : KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.
Author : Yung-Hao Wong, Tzong-Yi Lee, Han-Kuen Liang, Chia-Mao Huang, Ting-Yuan Wang, Yi-Huan Yang, Chia-Huei Chu, Hsien-Da Huang, Ming-Tat Ko and Jenn-Kang Hwang
Years : 2007
PubMed : 17517770

KinomeXplorer
Resource Type : Tool
Description :
KinomeXplorer is an integrated framework for modeling kinase-substrate interactions and aid in the design of inhibitor-based follow-up perturbation experiments. An interactive web interface allows investigation of predicted kinase-substrate interactions from human and major eukaryotic model organism ...
Taxonomy : N/A
Visit : http://kinomexplorer.info/

Publication Information

Article : KinomeXplorer: an integrated platform for kinome biology studies.
Author : Heiko Horn, Erwin M Schoof, Jinho Kim, Xavier Robin, Martin L Miller, Francesca Diella, Anita Palma, Gianni Cesareni, Lars Juhl Jensen & Rune Linding
Years : 2014
PubMed : 24874572

MetaPredPS
Resource Type : Tool
Description :
Remarkable morphological anomalies were observed in a female of Hoplopleura capitosa found on Mus musculus caught in Niemirówek, the Tomaszów district (Poland). The anomalies concerned the shape and chaetotaxis of some parapleural plates on the abdomen, constitute one of the basic taxonomical featur ...
Taxonomy : N/A
Visit : http://metapred.biolead.org/MetaPredPS/

Publication Information

Article : Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection.
Author : Ji Wan, Shuli Kang, Chuanning Tang, Jianhua Yan, Yongliang Ren, Jie Liu, Xiaolian Gao, Arindam Banerjee, Lynda B. M. Ellis and Tongbin Li
Years : 2008
PubMed : 1823471

Musite
Resource Type : Tool
Description :
To address the various limitations of current tools when applying to proteomes and to better utilize the large magnitude of experimentally verified phosphorylation sites, we developed a unique standalone application system Musite, specifically designed for large-scale prediction of both general and ...
Taxonomy : N/A
Visit : http://musite.sourceforge.net/

Publication Information

Article : Musite, a tool for global prediction of general and kinase-specific phosphorylation sites.
Author : Jianjiong Gao, Jay J. Thelen, A. Keith Dunker and Dong Xu
Years : 2010
PubMed : 20702892

NetPhorest
Resource Type : Tool
Description :
KinomeXplorer is an integrated framework for modeling kinase-substrate interactions and aid in the design of inhibitor-based follow-up perturbation experiments. An interactive web interface allows investigation of predicted kinase-substrate interactions from human and major eukaryotic model organism ...
Taxonomy : N/A
Visit : http://netphorest.info/

Publication Information

Article : Linear motif atlas for phosphorylation-dependent signaling.
Author : Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R.
Years : 2008
PubMed : 18765831

NetPhos
Resource Type : Tool
Description :
The Center for Biological Sequence Analysis at the Technical University of Denmark was formed in 1993, and conducts basic research in the field of bioinformatics and systems biology. The group of +90 scientists, working in ten specialist research groups, has a highly multi-disciplinary profile (mole ...
Taxonomy : Eukaryota
Visit : http://www.cbs.dtu.dk/services/NetPhos/

Publication Information

Article : Sequence and structure-based prediction of eukaryotic protein phosphorylation sites.
Author : Nikolaj Blom, Steen Gammeltoft2, Soren Brunak
Years : 1999
PubMed : 10600390

NetPhosK
Resource Type : Tool
Description :
The Center for Biological Sequence Analysis at the Technical University of Denmark was formed in 1993, and conducts basic research in the field of bioinformatics and systems biology. The group of +90 scientists, working in ten specialist research groups, has a highly multi-disciplinary profile (mole ...
Taxonomy : Eukaryota
Visit : http://www.cbs.dtu.dk/services/NetPhosK/

Publication Information

Article : Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence.
Author : Nikolaj Blom, Thomas Sicheritz-Pontén, Ramneek Gupta, Steen Gammeltoft andSoren Brunak
Years : 2004
PubMed : 15174133

NetPhosYeast
Resource Type : Tool
Description :
The Center for Biological Sequence Analysis at the Technical University of Denmark was formed in 1993, and conducts basic research in the field of bioinformatics and systems biology. The group of +90 scientists, working in ten specialist research groups, has a highly multi-disciplinary profile (mole ...
Taxonomy : Eukaryota, Fungi
Visit : http://www.cbs.dtu.dk/services/NetPhosYeast/

Publication Information

Article : NetPhosYeast: prediction of protein phosphorylation sites in yeast.
Author : Christian R. Ingrell, Martin L. Miller, Ole N. Jensen and Nikolaj Blom
Years : 2007
PubMed : 17282998

phos_pred
Resource Type : Tool
Description :
Reversible protein phosphorylation is one of the most important post-translational modifications, which regulates various biological cellular processes. Identification of the kinase-specific phosphorylation sites is helpful for understanding of phosphorylation mechanism and regulation processes. Alt ...
Taxonomy : N/A
Visit : http://bioinformatics.ustc.edu.cn/phos_pred/

Publication Information

Article : Prediction of protein kinase-specific phosphorylation sites in hierarchical structure using functional information and random forest
Author : Wenwen Fan, Xiaoyi Xu, Yi Shen, Huanqing Feng, Ao Li, Minghui Wang
Years : 2014
PubMed : 24452754

Phos3D
Resource Type : Tool
Description :
Phos3D is a web server for the prediction of phosphorylation sites (P-sites) in proteins, originally designed to investigate the advantages of including spatial information in P-site prediction. The approach is based on Support Vector Machines trained on sequence profiles enhanced by information fro ...
Taxonomy : N/A
Visit : http://phos3d.mpimp-golm.mpg.de/

Publication Information

Article : Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins.
Author : Pawel Durek, Christian Schudoma, Wolfram Weckwerth, Joachim Selbig and Dirk Walther
Years : 2009
PubMed : 19383128

PhoScan
Resource Type : Tool
Description :
Protein phosphorylation plays important roles in a variety of cellular processes. Detecting possible phosphorylation sites and their corresponding protein kinases is crucial for studying the function of many proteins. This article presents a new prediction system, called PhoScan, to predict phosphor ...
Taxonomy : N/A
Visit : http://bioinfo.au.tsinghua.edu.cn/phoscan/

Publication Information

Article : Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach.
Author : Tingting Li, Fei Li andXuegong Zhang
Years : 2008
PubMed : 17680694

PHOSFER
Resource Type : Tool
Description :
MOTIVATION: Phosphorylation is the most important post-translational modification in eukaryotes. Although many computational phosphorylation site prediction tools exist for mammals, and a few were created specifically for Arabidopsis thaliana, none are currently available for other plants. RESULTS: ...
Taxonomy : Eukaryota, Plants
Visit : http://saphire.usask.ca/saphire/phosfer/index.html

Publication Information

Article : Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights.
Author : Brett Trost and Anthony Kusalik
Years : 2013
PubMed : 23341503

PHOSITE
Resource Type : Tool
Description :
SUMMARY: The prediction of significant short functional protein sequences has inherent problems. In predicting phosphorylation sites, problems came from the shortness of phosphorylation sites, the difficulties in maintaining many different predefined models of binding sites, and the difficulties of ...
Taxonomy : N/A
Visit : http://www.phosite.com

Publication Information

Article : Highly specific prediction of phosphorylation sites in proteins
Author : Matthias Koenig and Niels Grabe
Years : 2004
PubMed : 15297298

PhosphoPICK
Resource Type : Tool
Description :
We're a bioinformatics group at the University of Queensland, Australia. Our research aims to develop, investigate and apply bioinformatics methodologies to understand and resolve a range of open problems in genomics, molecular and systems biology. Recent applications involve protein sorting, nuclea ...
Taxonomy : N/A
Visit : http://bioinf.scmb.uq.edu.au/phosphopick/phosphopick

Publication Information

Article : PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events
Author : Ralph Patrick1, Kim-Anh Lê Cao, Bostjan Kobe and Mikael Bodén
Years : 2015
PubMed : 25304781

PhosphoRice
Resource Type : Tool
Description :
PhosphoRice,a meta-predictor of rice-specific phosphorylation site, was constructed by integrating the newly phosphorylation sites predictors, NetPhos2.0, NetPhosK, Kinasephos, Scansite, Disphos and Predphosphos with parameters selected by restricted grid search and random search. It archieve an inc ...
Taxonomy : Eukaryota, Plants
Visit : https://github.com/PEHGP/PhosphoRice

Publication Information

Article : PhosphoRice: a meta-predictor of rice-specific phosphorylation sites
Author : Shufu Que, Kuan Li, Min Chen, Yongfei Wang, Qiaobin Yang, Wenfeng Zhang, Baoqian Zhang, Bangshu Xiong and Huaqin He
Years : 2012
PubMed : 22305189

PhosphoSVM
Resource Type : Tool
Description :
Phosphorylation is the most essential post-translational modification in eukaryotes and in particular plays a crucial role in a wide range of cellular processes. While, experiments on phosphorylation site discovery are time consuming and expensive to perform. Therefore, computational prediction meth ...
Taxonomy : N/A
Visit : http://sysbio.unl.edu/PhosphoSVM/

Publication Information

Article : PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine
Author : Yongchao Dou, Bo Yao, Chi Zhang
Years : 2014
PubMed : 24623121

pkaPS
Resource Type : Tool
Description :
BACKGROUND: Protein kinase A (cAMP-dependent kinase, PKA) is a serine/threonine kinase, for which ca. 150 substrate proteins are known. Based on a refinement of the recognition motif using the available experimental data, we wished to apply the simplified substrate protein binding model for accurate ...
Taxonomy : N/A
Visit : http://mendel.imp.ac.at/sat/pkaPS/

Publication Information

Article : pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model
Author : Georg Neuberger, Georg Schneider and Frank Eisenhaber
Years : 2007
PubMed : 17222345

PKIS
Resource Type : Tool
Description :
The increasingly huge gap of kinase-specific phosphorylation data hampers the reconstruction of signal transduction networks. Existing experimental methods and computational phosphorylation sites (P-sites) predictions tools have various limitations in addressing this problem. Here, based on the late ...
Taxonomy : N/A
Visit : http://bioinformatics.ustc.edu.cn/pkis/

Publication Information

Article : PKIS: computational identification of protein kinases for experimentally discovered protein phosphorylation sites
Author : Liang Zou, Mang Wang, Yi Shen, Jie Liao, Ao Li and Minghui Wang
Years : 2013
PubMed : 23941207

PlantPhos
Resource Type : Tool
Description :
Protein phosphorylation is the most widespread and well-studied post-translational modification in eukaryotic cells. It is one of the most prevalent intracellular protein modifications that influence numerous cellular processes (Steen, Jebanathirajah et al. 2006). It has been estimated that one-thir ...
Taxonomy : N/A
Visit : http://csb.cse.yzu.edu.tw/PlantPhos/

Publication Information

Article : PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity
Author : Tzong-Yi Lee, Neil Arvin Bretaña and Cheng-Tsung Lu
Years : 2011
PubMed : 21703007

PostMod
Resource Type : Tool
Description :
PostMod is a predict sever for phosphorylation sites. We develope new predict system soley sequence based approch. We combined physicochemical information ,motif information, and evolutionary information by simply comaparing sequence similarities. Taken together all those features we applied a novel ...
Taxonomy : N/A
Visit : http://pbil.kaist.ac.kr/PostMod

Publication Information

Article : PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship
Author : Inkyung Jung, Akihisa Matsuyama, Minoru Yoshida and Dongsup Kim
Years : 2010
PubMed : 20122181

PPRED
Resource Type : Tool
Description :
One of the most critical cellular phenomenon is phosphorylation of proteins as it is involved in signal transduction in various processes including cell cycle, proliferation and apoptosis. This phenomenon is catalyzed by protein kinases that affect certain acceptor residues (Serine, Threonine and Ty ...
Taxonomy : N/A
Visit : biomecis.uta.edu/~ashis/res/ppred/

Publication Information

Article : Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information
Author : Ashis Kumer Biswas, Nasimul Noman and Abdur Rahman Sikder
Years : 2010
PubMed : 20492656

PPSP
Resource Type : Tool
Description :
As a reversible and dynamic post-translational modification of proteins, phosphorylation plays an essential regulatory role in a broad spectrum of the biological cellular processes. Conventional experimental identifications of protein kinase (PK)-specific phosphorylation sites on substrates in vivo ...
Taxonomy : N/A
Visit : http://ppsp.biocuckoo.org/

Publication Information

Article : PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory
Author : Yu Xue, Ao Li, Lirong Wang, Huanqing Feng and Xuebiao Yao
Years : 2006
PubMed : 16549034

Predikin
Resource Type : Tool
Description :
Predikin is a system to predict substrate specificity of protein kinases. Some of the things Predikin can be used for include, Predict the most likely phosphorylation site for a specific protein kinase. Predict the most likely protein kinase for a phosphorylation site. Make predictions about WHOLE ...
Taxonomy : N/A
Visit : http://predikin.biosci.uq.edu.au/

Publication Information

Article : The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information
Author : Neil F. W. Saunders and Bostjan Kobe
Years : 2008
PubMed : 18477637

PredPhospho
Resource Type : Tool
Description :
MOTIVATION: Phosphorylation is involved in diverse signal transduction pathways. By predicting phosphorylation sites and their kinases from primary protein sequences, we can obtain much valuable information that can form the basis for further research. Using support vector machines, we attempted to ...
Taxonomy : N/A
Visit : http://www.ngri.re.kr/ proteo/PredPhospho.htm

Publication Information

Article : Prediction of phosphorylation sites using SVMs
Author : Kim JH, Lee J, Oh B, Kimm K, Koh I
Years : 2004
PubMed : 15231530

PSEA
Resource Type : Tool
Description :
Protein phosphorylation catalysed by kinases plays crucial regulatory roles in intracellular signal transduction. With the increasing number of kinase-specific phosphorylation sites and disease-related phosphorylation substrates that have been identified, the desire to explore the regulatory relatio ...
Taxonomy : Eukaryota, Animals
Visit : http://bioinfo.ncu.edu.cn/PKPred_Home.aspx

Publication Information

Article : PSEA: Kinase-specific prediction and analysis of human phosphorylation substrates
Author : Sheng-Bao Suo, Jian-Ding Qiu, Shao-Ping Shi, Xiang Chen and Ru-Ping Liang
Years : 2014
PubMed : 24681538

PTMPred
Resource Type : Tool
Description :
Recent efforts to develop a universal view of complex networks have created both excitement and confusion about the way in which knowledge of network structure can be used to understand, control, or design system behavior. This paper offers perspective on the emerging field of “network science” in t ...
Taxonomy : N/A
Visit : http://doc.aporc.org/wiki/PTMPred

Publication Information

Article : Prediction of posttranslational modification sites from amino acid sequences with kernel methods
Author : Yan Xua, Xiaobo Wangb, Yongcui Wangb, Yingjie Tianc, Xiaojian Shaod, Ling-Yun Wue, Naiyang Deng
Years : 2014
PubMed : 24291233

RLIMS-P
Resource Type : Tool
Description :
RLIMS-P is a rule-based text-mining program specifically designed to extract protein phosphorylation information on protein kinase, substrate and phosphorylation sites from biomedical literature (Hu et al., 2005). RLIMS-P currently works on PubMed abstracts and open access full text articles. ...
Taxonomy : N/A
Visit : http://research.bioinformatics.udel.edu/rlimsp/

Publication Information

Article : RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information
Author : Manabu Torii1, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Çelen, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker and Cathy H. Wu
Years : 2014
PubMed : 25122463

ViralPhos
Resource Type : Tool
Description :
ViralPhos is a web server for identifying potential virus phosphorylation sites with substrate motifs. Phosphorylation of virus proteins is linked to viral replication, which leads to an inhibition of normal host-cell functions. This has motivated the field to further elucidate the process of phosp ...
Taxonomy : Viruses
Visit : http://csb.cse.yzu.edu.tw/ViralPhos/

Publication Information

Article : ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins
Author : Kai-Yao Huang, Cheng-Tsung Lu, Neil Arvin Bretaña, Tzong-Yi Lee and Tzu-Hao Chang
Years : 2013
PubMed : 24564381