PTM Related Resources

PTM : ALL        Type : ALL

EnsembleGly
Resource Type : Tool
Description :
BACKGROUND: Glycosylation is one of the most complex post-translational modifications (PTMs) of proteins in eukaryotic cells. Glycosylation plays an important role in biological processes ranging from protein folding and subcellular localization, to ligand recognition and cell-cell interactions. Exp ...
Taxonomy : N/A
Visit : http://turing.cs.iastate.edu/EnsembleGly/

Publication Information

Article : Glycosylation site prediction using ensembles of Support Vector Machine classifiers.
Author : Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs and Vasant Honavar
Years : 2007
PubMed : 17996106

GlycoEpitope
Resource Type : DB
Description :
Carbohydrate chains occupy truly significant positions in various fields of life sciences and biotechnology. Recently, the wide-ranging involvement of carbohydrate chains in life sciences has been extended to such diverse functions as cell to cell recognition and communication in neuronal tissues an ...
Taxonomy : N/A
Visit : http://www.glycoepitope.jp/

Publication Information

Article : GlycoEpitope: A Database of Carbohydrate Epitopes and Antibodies
Author : Toshisuke Kawasaki, Hiromi Nakao, Tomoko Tominaga
Years : 2008
PubMed :

GlycoFish
Resource Type : DB
Description :
LIPID PROFILING & CELL ENGINEERING POST-DOCTORAL SCIENTIST An opening for a motivated and talented post-doctoral scientist in lipid profiling/ lipidomics and cellular engineering is available in the laboratory of Dr. Betenbaugh. Candidates should have a PhD in biochemistry, molecular biology, bioe ...
Taxonomy : Eukaryota, Animals
Visit : http://betenbaugh.jhu.edu/GlycoFish/

Publication Information

Article : GlycoFish: a database of zebrafish N-linked glycoproteins identified using SPEG method coupled with LC/MS.
Author : Deniz Baycin-Hizal , Yuan Tian , Ilhan Akan , Elena Jacobson , Dean Clark , Alexander Wu , Russell Jampol , Karen Palter Michael Betenbaugh , and Hui Zhang
Years : 2011
PubMed : 21591763

GlycoFly
Resource Type : DB
Description :
LIPID PROFILING & CELL ENGINEERING POST-DOCTORAL SCIENTIST An opening for a motivated and talented post-doctoral scientist in lipid profiling/ lipidomics and cellular engineering is available in the laboratory of Dr. Betenbaugh. Candidates should have a PhD in biochemistry, molecular biology, bioe ...
Taxonomy : Eukaryota, Animals
Visit : http://betenbaugh.jhu.edu/GlycoFly/

Publication Information

Article : GlycoFly: a database of Drosophila N-linked glycoproteins identified using SPEG--MS techniques.
Author : Deniz Baycin-Hizal , Yuan Tian , Ilhan Akan , Elena Jacobson , Dean Clark , Jeffrey Chu , Karen Palter , Hui Zhang , and Michael . Betenbaugh
Years : 2011
PubMed : 21480662

GlycomeDB
Resource Type : DB
Description :
Carbohydrates are the third major class of biological macromolecules, besides proteins and DNA molecules. They are involved in numerous biological processes, among them protein folding and inter/intra cell recognition. In contrast to DNA and proteins neither a comprehensive database for carbohydrate ...
Taxonomy : N/A
Visit : http://www.glycome-db.org/

Publication Information

Article : GlycomeDB--a unified database for carbohydrate structures.
Author : René Ranzinger, Stephan Herget, Claus-Wilhelm von der Lieth and Martin Frank
Years : 2011
PubMed : 21045056

GlycoMine
Resource Type : Tool
Description :
Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes such as cellular communication, ligand recognition, and subcellular recognition. It is estimated that >50% of the entire human proteome is ...
Taxonomy : N/A
Visit : http://www.structbioinfor.org/Lab/GlycoMine/

Publication Information

Article : GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.
Author : Fuyi Li, Chen Li, Mingjun Wang, Geoffrey I. Webb, Yang Zhang, James C. Whisstock and Jiangning Song
Years : 2015
PubMed : 25568279

GlycoPP
Resource Type : Tool
Description :
Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes such as cellular communication, ligand recognition, and subcellular recognition. It is estimated that >50% of the entire human proteome is ...
Taxonomy : Archaea, Bacteria
Visit : http://www.imtech.res.in/raghava/glycopp/

Publication Information

Article : GlycoPP: a webserver for prediction of N- and O-glycosites in prokaryotic protein sequences.
Author : Jagat S. Chauhan, Adil H. Bhat, Gajendra P. S. Raghava , Alka Rao
Years : 2012
PubMed : 22808107

GlycoProtDB
Resource Type : DB
Description :
GlycoProtDB is a glycoprotein database providing information of Asn (N)-glycosylated proteins and their glycosylated site(s), which were constructed by employing a bottom-up strategy using actual glycopeptide sequences identified by LC/MS-based glycoproteomic technologies. Current contents are glyco ...
Taxonomy : N/A
Visit : http://jcggdb.jp/rcmg/gpdb/index.action

Publication Information

Article : Large-scale identification of N-glycosylated proteins of mouse tissues and construction of a glycoprotein database, GlycoProtDB.
Author : Hiroyuki Kaji , Toshihide Shikanai , Akiko Sasaki-Sawa , Hongling Wen , Mika Fujita , Yoshinori Suzuki , Daisuke Sugahara , Hiromichi Sawaki , Yoshio Yamauchi , Takashi Shinkawa , Masato Taoka , Nobuhiro Takahashi , Toshiaki Isobe , and Hisashi Narimatsu
Years : 2012
PubMed : 22823882

UnicarbKB
Resource Type : DB
Description :
UniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the ...
Taxonomy : N/A
Visit : http://unicarbkb.org

Publication Information

Article : UniCarbkb: building a knowledge platform for glycoproteomics
Author : Matthew P. Campbell, Robyn Peterson, Julien Mariethoz, Elisabeth Gasteiger, Yukie Akune, Kiyoko F. Aoki-Kinoshita, Frederique Lisacek and Nicolle H. Packer
Years : 2014
PubMed : 24234447

GLYCOSCIENCES.de
Resource Type : DB
Description :
The human genome seems to encode for not more than 30,000 to 40,000 proteins. A major challenge is to understand how posttranslational events, such as glycosylation, affect the activities and functions of these proteins in health and disease. The importance of protein glycosylation is becoming widel ...
Taxonomy : N/A
Visit : http://www.glycosciences.de/

Publication Information

Article : GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research.
Author : Thomas Lütteke, Andreas Bohne-Lang, Alexander Loss,Thomas Goetz, Martin Frank, and Claus-W. von der Lieth
Years : 2006
PubMed : 16239495

GlycoSuiteDB
Resource Type : DB
Description :
UniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the ...
Taxonomy : N/A
Visit : http://www.unicarbkb.org/

Publication Information

Article : GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources.
Author : Catherine A. Cooper, Hiren J. Joshi, Mathew J. Harrison, Marc R. Wilkins and Nicolle H. Packer
Years : 2003
PubMed : 12520065

GPP
Resource Type : Tool
Description :
Ab Initio Calculations of the Electronic Excited States of Molecules, Electronic Structure and Circular Dichroism of Proteins, Protein Folding and Evolution, Bioinformatics, Computer-Aided Drug Design, Drug Resistance. Please follow the links to publications on the respective topic. ...
Taxonomy : N/A
Visit : http://comp.chem.nottingham.ac.uk/glyco/

Publication Information

Article : Prediction of glycosylation sites using random forests.
Author : Stephen E Hamby and Jonathan D Hirst
Years : 2008
PubMed : 19038042

GS-align
Resource Type : Tool
Description :
Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. GS-align is a novel computational method for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan struc ...
Taxonomy : N/A
Visit : http://www.glycanstructure.org/gsalign

Publication Information

Article : GS-align for glycan structure alignment and similarity measurement.
Author : Hui Sun Lee, Sunhwan Jo, Srayanta Mukherjee, Sang-Jun Park, Jeffrey Skolnick, Jooyoung Lee and Wonpil Im
Years : 2015
PubMed : 25857669

GlycoEP
Resource Type : Tool
Description :
Glycosylation is one of the most abundant and an important post-translational modification of proteins. Glycosylated proteins (glycoproteins) are involved in various cellular biological functions like protein folding, cell-cell interactions, cell recognition and host-pathogen interactions. A large n ...
Taxonomy : Eukaryota
Visit : http://www.imtech.res.in/raghava/glycoep

Publication Information

Article : In silico Platform for Prediction of N-, O- and C-Glycosites in Eukaryotic Protein Sequences
Author : Jagat Singh Chauhan, Alka Rao, Gajendra P. S. Raghava
Years : 2013
PubMed : 23840574

CFG
Resource Type : DB
Description :
The CFG's Glycan Structures Database offers detailed structural and chemical information for thousands of glycans, including both synthetic glycans and glycans isolated from biological sources. Each glycan structure in the database is linked to relevant entries in CFG and external databases (includi ...
Taxonomy : N/A
Visit : http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/carbMoleculeHome.jsp

Publication Information

Article : Glycan array data management at Consortium for Functional Glycomics.
Author : Maha Venkataraman, Ram Sasisekharan, Rahul Raman
Years : 2015
PubMed : 25753711

ProGlycProt
Resource Type : DB
Description :
ProGlycProt (Prokaryotic Glycoproteins) is a manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused beginning of an effort to provide concise relevant informati ...
Taxonomy : Prokaryotes
Visit : http://www.proglycprot.org/

Publication Information

Article : ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins.
Author : Aadil H. Bhat, Homchoru Mondal, Jagat S. Chauhan, Gajendra P. S. Raghava, Amrish Methi and Alka Rao
Years : 2012
PubMed : 22039152

NetNGlyc
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, Animals
Visit : http://www.cbs.dtu.dk/services/NetNGlyc/

Publication Information

Article : NetNGlyc: Prediction of N-glycosylation sites in human proteins
Author : R Gupta, E Jung, S Brunak
Years : 2004
PubMed :

UniPep
Resource Type : DB
Description :
Unipep is a project to provide access to proteomics data from the Serum Biomarker group at the Swiss Federal Institute of Technology (ETH) in Zurich Switzerland, and the Institute for Systems Biology (ISB) in Seattle, Washington USA. In the initial phase, we provide a searchable interface to a libr ...
Taxonomy : Eukaryota, Animals
Visit : http://www.unipep.org/

Publication Information

Article : UniPep--a database for human N-linked glycosites: a resource for biomarker discovery.
Author : Hui Zhang, Paul Loriaux, Jimmy Eng, David Campbell, Andrew Keller, Pat Moss, Richard Bonneau, Ning Zhang, Yong Zhou, Bernd Wollscheid, Kelly Cooke, Eugene C Yi, Hookeun Lee, Elaine R Peskind, Jing Zhang, Richard D Smith and Ruedi Aebersold
Years : 2006
PubMed : 16901351

GECS
Resource Type : Tool
Description :
About GECS GECS (Gene Expression to Chemical Structure) is a collection of prediction methods linking genomic or transcriptomic contents of genes to chemical structures of biosynthetic substances. This N-Glycan Prediction Server is based on the repertoire of glycosyltransferases for N-glycan biosyn ...
Taxonomy : N/A
Visit : http://www.genome.jp/tools/gecs/

Publication Information

Article : Prediction of glycan structures from gene expression data based on glycosyltransferase reactions
Author : Shin Kawano, Kosuke Hashimoto, Takashi Miyama, Susumu Goto and Minoru Kanehisa
Years : 2005
PubMed : 16159923

dbOGAP
Resource Type : DB
Description :
Introduction: Protein O-GlcNAcylation is an O-linked glycosylation involving attachment of beta-N-acetylglucosamine (GlcNAc) to Ser/Thr residues catalyzed by O-GlcNAc transferase (OGT) without further extension of GlcNAc, whose removal is catalyzed by O-GlcNAcase (OGA). Unlike N-linked and mucin-typ ...
Taxonomy : Animals
Visit : http://cbsb.lombardi.georgetown.edu/hulab/OGAP.html

Publication Information

Article : dbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation.
Author : Jinlian Wang, Manabu Torii, Hongfang Liu, Gerald W Hart and Zhang-Zhi Hu
Years : 2011
PubMed : 21466708

YinOYang
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/YinOYang/

Publication Information

Article : Prediction of glycosylation across the human proteome and the correlation to protein function.
Author : Gupta R, Brunak S
Years : 2002
PubMed : 11928486

DictyOGlyc
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 : N/A
Visit : http://www.cbs.dtu.dk/services/DictyOGlyc/

Publication Information

Article : Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks.
Author : Ramneek Gupta, Eva Jung, Andrew A. Gooley, Keith L. Williams, Søren Brunak1 and Jan Hansen
Years : 1999
PubMed : 10521537

O-GlycBase
Resource Type : DB
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 : N/A
Visit : http://www.cbs.dtu.dk/databases/OGLYCBASE/

Publication Information

Article : O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.
Author : Ramneek Gupta, Hanne Birch, Kristoffer Rapacki, Soren Brunak and Jan E. Hansen
Years : 1999
PubMed : 9847232

NetOGlyc
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, Animals
Visit : http://www.cbs.dtu.dk/services/NetOGlyc/

Publication Information

Article : Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology.
Author : Catharina Steentoft, Sergey Y Vakhrushev, Hiren J Joshi, Yun Kong, Malene B Vester?Christensen, Katrine T?B G Schjoldager, Kirstine Lavrsen, Sally Dabelsteen, Nis B Pedersen, Lara Marcos?Silva, Ramneek Gupta, Eric Paul Bennett, Ulla Mandel, Søren Brunak, Hans H Wandall, Steven B Levery, Henrik Clausen
Years : 2013
PubMed : 23584533

Oglyc
Resource Type : Tool
Description :
O-glycosylation is one of the most important, frequent and complex post-translational modifications. This modification can activate and affect protein functions. Here, we present three support vector machines models based on physical properties, 0/1 system, and the system combining the above two fea ...
Taxonomy : N/A
Visit : http://www.biosino.org/Oglyc/

Publication Information

Article : Predicting  O-glycosylation sites in mammalian proteins by using SVMs
Author : Sujun Li, Boshu Liu, Rong Zeng, Yudong Cai, Yixue Li
Years : 2006
PubMed : 16731044

big-Pi plant
Resource Type : Tool
Description :
Posttranslational glycosylphosphatidylinositol (GPI) lipid anchoring is common not only for animal and fungal but also for plant proteins. The attachment of the GPI moiety to the carboxyl-terminus after proteolytic cleavage of a C-terminal propeptide is performed by the transamidase complex. Its fou ...
Taxonomy : Eukaryota
Visit : http://mendel.imp.ac.at/gpi/plant_server.html

Publication Information

Article : Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice
Author : Birgit Eisenhaber, Michael Wildpaner, Carolyn J. Schultz, Georg H.H. Borner, Paul Dupree and Frank Eisenhaber
Years : 2003
PubMed : 14681532

FragAnchor
Resource Type : Tool
Description :
A glycosylphosphatidylinositol (GPI) anchor is a common but complex C-terminal post-translational modification of extracellular proteins in eukaryotes. Here we investigate the problem of correctly annotating GPI-anchored proteins for the growing number of sequences in public databases. We developed ...
Taxonomy : Eukaryota
Visit : http://navet.ics.hawaii.edu/~fraganchor/NNHMM/NNHMM.html

Publication Information

Article : FragAnchor: a large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring
Author : Guylaine Poisson, Cedric Chauve, Xin Chen, Anne Bergeron
Years : 2007
PubMed : 17893077

GPI-SOM
Resource Type : Tool
Description :
MOTIVATION: Anchoring of proteins to the extracytosolic leaflet of membranes via C-terminal attachment of glycosylphosphatidylinositol (GPI) is ubiquitous and essential in eukaryotes. The signal for GPI-anchoring is confined to the C-terminus of the target protein. In order to identify anchoring sig ...
Taxonomy : Eukaryota
Visit : http://gpi.unibe.ch/

Publication Information

Article : Identification of GPI anchor attachment signals by a Kohonen self-organizing map
Author : Niklaus Fankhauser and Pascal Mäser
Years : 2005
PubMed : 15691858

PredGPI
Resource Type : Tool
Description :
PredGPI is a prediction system for GPI-anchored proteins. It is based on a support vector machine (SVM) for the discrimination of the anchoring signal, and on a Hidden Markov Model (HMM) for the prediction of the most probable omega-site ...
Taxonomy : Eukaryota
Visit : http://gpcr.biocomp.unibo.it/predgpi/index.htm

Publication Information

Article : PredGPI: a GPI-anchor predictor
Author : Andrea Pierleoni, Pier Luigi Martelli and Rita Casadio
Years : 2008
PubMed : 18811934

NetAcet
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 : N/A
Visit : http://www.cbs.dtu.dk/services/NetAcet/

Publication Information

Article : NetAcet: prediction of N-terminal acetylation sites.
Author : Lars Kiemer, Jannick Dyrløv Bendtsen and Nikolaj Blom
Years : 2005
PubMed : 15539450

N-Ace
Resource Type : Tool
Description :
N-Ace is a web tool for predicting the protein Acetylation site based on Support Vector Machine (SVM), which is training depend on the amino acid sequence and other structural characteristics, such as accessible surface area, absolute entropy, non-bonded energy, size, amino acid composition, steric ...
Taxonomy : N/A
Visit : http://N-Ace.mbc.NCTU.edu.tw/

Publication Information

Article : N-Ace: using solvent accessibility and physicochemical properties to identify protein N-acetylation sites.
Author : Tzong-Yi Lee,Justin Bo-Kai Hsu, Feng-Mao Lin2, Wen-Chi Chang, Po-Chiang Hsu andHsien-Da Huang
Years : 2010
PubMed : 20839302

CPLA
Resource Type : DB
Description :
CPLM (Compendium of Protein Lysine Modifications) is an online data resource specifically designed for protein lysine modifications (PLMs). The CPLM database was extended and adapted from our CPLA 1.0 (Compendium of Protein Lysine Acetylation) database (Liu et al., 2011), and the 2.0 release contain ...
Taxonomy : N/A
Visit : http://cpla.biocuckoo.org

Publication Information

Article : CPLA 1.0: an integrated database of protein lysine acetylation
Author : Zexian Liu, Jun Cao, Xinjiao Gao, Yanhong Zhou,Longping Wen, Xiangjiao Yang, Xuebiao Yao,Jian Ren and Yu Xue
Years : 2010
PubMed : 21059677

LysAcet
Resource Type : Tool
Description :
Reversible acetylation on lysine residues, a crucial post-translational modification (PTM) for both histone and non-histone proteins, governs many central cellular processes. Due to limited data and lack of a clear acetylation consensus sequence, little research has focused on prediction of lysine a ...
Taxonomy : N/A
Visit : http://www.biosino.org/LysAcet/

Publication Information

Article : Improved Prediction of Lysine Acetylation by Support Vector Machines
Author : Songling Li, Hong Li, Mingfa Li, Yu Shyr, Lu Xie and Yixue Li - See more at: http://www.eurekaselect.com/84739/article#sthash.P9H2djtQ.dpuf
Years : 2009
PubMed : 19689425

ASEB
Resource Type : Tool
Description :
Protein lysine acetylation plays an important role in the normal functioning of cells, including gene expression regulation, protein stability and metabolism regulation. Although large amounts of lysine acetylation sites have been identified via large-scale mass spectrometry or traditional experimen ...
Taxonomy : N/A
Visit : http://cmbi.bjmu.edu.cn/huac

Publication Information

Article : ASEB: a web server for KAT-specific acetylation site prediction
Author : Likun Wang,Yipeng Du,Ming Lu and Tingting Li
Years : 2012
PubMed : 22600735

BRABSB-PHKA
Resource Type : Tool
Description :
BRABSB-PHKA is an in silico online tool for Prediction of potential Human Lysine(K) Acetylation(PHKA) sites from protein sequences. The computational methodology is based on Bi-Relative Binomial Score Bayes (BRBSB) combined with support vector machines (SVMs). BRBSB-PHKA yields, on average, a sensit ...
Taxonomy : N/A
Visit : http://www.bioinfo.bio.cuhk.edu.hk/bpbphka

Publication Information

Article : Systematic analysis of human lysine acetylation proteins and accurate prediction of human lysine acetylation through bi-relative adapted binomial score Bayes feature representation
Author : Jianlin Shao, Dong Xu, Landian Hu, Yiu-Wa Kwan, Yifei Wang, Xiangyin Kong and Sai-Ming Ngai
Years :
PubMed : 22936054

PAIL
Resource Type : Tool
Description :
Protein acetylation is a widespread covalent modification in eukaryotes, transferring acetyl groups from acetyl coenzyme A (acetyl CoA) to either ?-amino (N?) group of amino-terminal residues or to the ?-amino group (N?) of internal lysines at specific sites (Glozak,MA et al., 2005;Kouzarides,T, 200 ...
Taxonomy : N/A
Visit : http://bdmpail.biocuckoo.org/prediction.php

Publication Information

Article : Prediction of N?-acetylation on internal lysines implemented in Bayesian Discriminant Method
Author : Ao Li, Yu Xue, Changjiang Jin, Minghui Wang, Xuebiao Yao
Years : 2006
PubMed : 17045240

LAceP
Resource Type : Tool
Description :
Lysine acetylation is a crucial type of protein post-translational modification, which is involved in many important cellular processes and serious diseases. However, identification of protein acetylated sites through traditional experiment methods is time-consuming and laborious. Those methods are ...
Taxonomy : N/A
Visit : http://www.scbit.org/iPTM/

Publication Information

Article : LAceP: Lysine Acetylation Site Prediction Using Logistic Regression Classifiers
Author : Ting Hou, Guangyong Zheng, Pingyu Zhang,Jia Jia, Jing Li, Lu Xie, Chaochun Wei and Yixue Li,Wei-Guo Zhu
Years : 2014
PubMed : 24586884

PSKAcePred
Resource Type : Tool
Description :
In the prediction model PSKAcePred, the sequences fragments are firstly extracted in window size -10 to +10 (acetylation lysine centered in position of 0). Then, 13 optimization positions are chosen by using position-specific method. Users can submit protein sequence(s) in FASTA format to this web i ...
Taxonomy : N/A
Visit : http://bioinfo.ncu.edu.cn/inquiries_PSKAcePred.aspx

Publication Information

Article : Position-specific analysis and prediction for protein lysine acetylation based on multiple features.
Author : Sheng-Bao Suo, Jian-Ding Qiu , Shao-Ping Shi, Xing-Yu Sun, Shu-Yun Huang, Xiang Chen, Ru-Ping Liang
Years : 2012
PubMed : 23173045

CarSPred
Resource Type : Tool
Description :
Introduction: 1.The software CarSPred could be used to identify carbonylation sites of query human protein sequences. 2.The software consists of four modules which are devoted to K, R, T and P carbonylation site prediction separately. 3.It receives protein sequences or file in FASTA format as input. ...
Taxonomy : Eukaryota, Animals
Visit : http://sourceforge.net/projects/hqlstudio/files/CarSPred-1.0/

Publication Information

Article : CarSPred: a computational tool for predicting carbonylation sites of human proteins.
Author : Hongqiang Lv, Jiuqiang Han , Jun Liu , Jiguang Zheng, Ruiling Liu, Dexing Zhong
Years : 2014
PubMed : 25347395

CPLM
Resource Type : DB
Description :
CPLM (Compendium of Protein Lysine Modifications) is an online data resource specifically designed for protein lysine modifications (PLMs). The CPLM database was extended and adapted from our CPLA 1.0 (Compendium of Protein Lysine Acetylation) database (Liu et al., 2011), and the 2.0 release contain ...
Taxonomy : N/A
Visit : http://cplm.biocuckoo.org/

Publication Information

Article : CPLM: a database of protein lysine modifications.
Author : Zexian Liu, Yongbo Wang, Tianshun Gao, Zhicheng Pan, Han Cheng, Qing Yang, Zhongyi Cheng2, Anyuan Guo, Jian Ren and Yu Xue
Years : 2014
PubMed : 24214993

CrosstalkDB
Resource Type : DB
Description :
This database aims to collect mass spectrometry data of multiply modified histones or histone tails. You can search, analyze and download data from this database without having to log in. Quantification can be based on either spectral counting or peak intensities. We recommend isoScale and Histon ...
Taxonomy : N/A
Visit : http://crosstalkdb.bmb.sdu.dk/

Publication Information

Article : Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk
Author : Veit Schwammle, Claudia-Maria Aspalter, Simone Sidoli,and Ole N. Jensen
Years : 2014
PubMed : 24741113

dbPTM
Resource Type : DB
Description :
Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high-throughput of mass spectrometry-based methods in identifying site-specifi ...
Taxonomy : N/A
Visit : http://dbptm.mbc.nctu.edu.tw/index.php

Publication Information

Article : DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.
Author : Cheng-Tsung Lu, Kai-Yao Huang, Min-Gang Su, Tzong-Yi Lee, Neil Arvin Bretana, Wen-Chi Chang, Yi-Ju Chen, Yu-Ju Chen and Hsien-Da Huang
Years : 2013
PubMed : 23193290

HIstome
Resource Type : DB
Description :
Post-translational modification (PTM) of histones is a crucial step in epigenetic regulation of a gene. N-terminal tails of histones are the most accessible regions of these peptide as they protrude from the nucleosome and possess no specific structure. These tails are subjected to various modificat ...
Taxonomy : Eukaryota, Animals
Visit : http://www.actrec.gov.in/histome/ptm_main.php

Publication Information

Article : HIstome--a relational knowledgebase of human histone proteins and histone modifying enzymes.
Author : Satyajeet P. Khare, Farhat Habib, Rahul Sharma, Nikhil Gadewal, Sanjay Gupta and Sanjeev Galande
Years : 2012
PubMed : 22140112

ISSPred
Resource Type : Tool
Description :
In the modern era, process of protein expression is further complexed by the addition of new Post-translational Modification events such as proteolytic cleavage of polyproteins, proteome mediated peptide ligation, non-ribosomal addition of moieties and intein mediated protein splicing. Protein spli ...
Taxonomy : N/A
Visit : http://www.imtech.res.in/raghava/isspred/

Publication Information

Article : ISSPred: Identification of Intein proteins and their Splice Sites
Author : Hifzur Rahman Ansari
Years : 2008
PubMed :

ModPred
Resource Type : Tool
Description :
ModPred is a sequence-based predictor of potential post-translational modification (PTM) sites in proteins. It consists of 34 ensembles of logistic regression models, trained separately on a combined set of 126,036 non-redundant experimentally verified sites for 23 different modifications, obtained ...
Taxonomy : N/A
Visit : http://www.modpred.org/

Publication Information

Article : The structural and functional signatures of proteins that undergo multiple events of post-translational modification
Author : Vikas Pejaver, Wei-Lun Hsu, Fuxiao Xin, A. Keith Dunker, Vladimir N. Uversky and Predrag Radivojac
Years : 2014
PubMed : 24888500

Motifs tree
Resource Type : Tool
Description :
MOTIVATION: Post-translational modifications (PTMs) are important steps in the maturation of proteins. Several models exist to predict specific PTMs, from manually detected patterns to machine learning methods. On one hand, the manual detection of patterns does not provide the most efficient classif ...
Taxonomy : N/A
Visit : http://terminus.unige.ch/

Publication Information

Article : Motifs tree: a new method for predicting post-translational modifications.
Author : Christophe Charpilloz, Anne-Lise Veuthey, Bastien Chopard and Jean-Luc Falcone
Years : 2014
PubMed : 24681905

NetChop
Resource Type : Tool
Description :
NetChop 3.1 Server The NetChop server produces neural network predictions for cleavage sites of the human proteasome. NetChop has been trained on human data only, and will therefore presumably have better performance for prediction of the cleavage sites of the human proteasome. However, since the ...
Taxonomy : N/A
Visit : http://www.cbs.dtu.dk/services/NetChop/

Publication Information

Article : Prediction of proteasome cleavage motifs by neural networks.
Author : Can Ke?mir, Alexander K. Nussbaum, Hansjörg Schild, Vincent Detours and Søren Brunak
Years : 2002
PubMed : 11983929

NetCorona
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 : Viruses
Visit : http://www.cbs.dtu.dk/services/NetCorona/

Publication Information

Article : Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology.
Author : Lars Kiemer, Ole Lund, Søren Brunak and Nikolaj Blom
Years : 2004
PubMed : 15180906

NetPicoRNA
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 : Viruses
Visit : http://www.cbs.dtu.dk/services/NetPicoRNA/

Publication Information

Article : Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks.
Author : Nikolaj Blom, Jan Hansen, Søren Brunak1 andDieter Blaas
Years : 1996
PubMed : 8931139

novPTMenzy
Resource Type : DB
Description :
Several attempts have been made to catalog the wealth of available information on Post-Translational Modification(PTMs) for easy retrieval and analysis. However, the tools and databases available mainly focus on modified sites or enzymes of well-known PTMs. Tools for newly discovered PTMs like AMPyl ...
Taxonomy : N/A
Visit : http://www.nii.ac.in/novptmenzy.html

Publication Information

Article : novPTMenzy: a database for enzymes involved in novel post-translational modifications.
Author : Shradha Khater and Debasisa Mohanty
Years : 2015
PubMed : 25931459

PAProC
Resource Type : Tool
Description :
What are proteasomes ? Proteasomes are cytosolic multisubunit proteases which are involved in cell cycle control, transcription factor activation and the generation of peptide ligands for MHC I molecules (for reviews, see Baumeister et al. (1998), Rock & Goldberg (1999), Uebel & Tampe (1999)). They ...
Taxonomy : Eukaryota, Animals, Fungi
Visit : http://paproc.de/

Publication Information

Article : PAProC: a prediction algorithm for proteasomal cleavages available on the WWW.
Author : Nussbaum AK, Kuttler C, Hadeler KP, Rammensee HG, Schild H
Years : 2001
PubMed : 11345595

Pcleavage
Resource Type : Tool
Description :
Antigen processing and presentation are processes that occur within a cell that result in fragmentation (proteolysis) of proteins, association of the fragments with MHC molecules, and expression of the peptide-MHC molecules at the cell surface where they can be recognized by the T cell receptor on a ...
Taxonomy : N/A
Visit : http://www.imtech.res.in/raghava/pcleavage/index.html

Publication Information

Article : Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences.
Author : Bhasin M, Raghava GP
Years : 2005
PubMed : 15988831

PEIMAN
Resource Type : Tool
Description :
PEIMAN (Posttranslational modification Enrichment, Integration and Matching ANalysis) is a standalone software and platform free for enrichment analysis in post translational modification (PTM) types. The software also provides the comparison between two different lists of proteins, focusing on PTM ...
Taxonomy : N/A
Visit : http://bs.ipm.ir/softwares/PEIMAN/

Publication Information

Article : PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis
Author : Payman Nickchi, Mohieddin Jafari and Shiva Kalantari
Years : 2015
PubMed : 25911152

PeptideMap
Resource Type : Tool
Description :
PeptideMap marks a peptide sequence at every position where a known proteolytic enzyme or reagent might cut it. You can select one or a few enzymes or let PeptideMap use the whole list. PeptideMap is simply the program Map run with -PROGRAMname=PeptideMap. (See the documentation for Map in the Prog ...
Taxonomy : N/A
Visit : http://prowl.rockefeller.edu/prowl/peptidemap.html

Publication Information

Article :
Author :
Years :
PubMed :

PHOXTRACK
Resource Type : Tool
Description :
PHOXTRACK (PHOsphosite-X-TRacing Analysis of Causal Kinases) is a computational tool to compare kinase activities between different phosphoproteomes to identify key regulating proteins. In its current version, PHOXTRACK maps quantified phosphopeptides to their putative kinases and tests for concorda ...
Taxonomy : N/A
Visit : http://phoxtrack.molgen.mpg.de/

Publication Information

Article : PHOXTRACK-a tool for interpreting comprehensive datasets of post-translational modifications of proteins.
Author : Christopher Weidner, Cornelius Fischer and Sascha Sauer
Years : 2014
PubMed : 25152232

ProP
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 : N/A
Visit : http://www.cbs.dtu.dk/services/ProP/

Publication Information

Article : Prediction of proprotein convertase cleavage sites.
Author : Peter Duckert, Søren Brunak and Nikolaj Blom
Years : 2004
PubMed : 14985543

ProteomeScout
Resource Type : DB
Description :
ProteomeScout is a database of proteins and post-translational modifications. There are two main data types in ProteomeScout. 1) Proteins: Visualize proteins or annotate your own proteins. 2) Experiments: You can load a new experiment or browse and analyze an existing experiment. ...
Taxonomy : N/A
Visit : https://proteomescout.wustl.edu/

Publication Information

Article : ProteomeScout: a repository and analysis resource for post-translational modifications and proteins.
Author : Matthew K. Matlock, Alex S. Holehouse and Kristen M. Naegle
Years : 2015
PubMed : 25414335

PSP
Resource Type : DB
Description :
PhosphoSitePlus® (PSP) is an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, ubiquitination, acetylation and methylation. See About PhosphoSite above for more information. Please ...
Taxonomy : Eukaryota, Animals
Visit : http://www.phosphosite.org/homeAction.do

Publication Information

Article : PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.
Author : Peter V. Hornbeck, Bin Zhang, Beth Murray, Jon M. Kornhauser, Vaughan Latham and Elzbieta Skrzypek
Years : 2015
PubMed : 25514926

PTMCode
Resource Type : DB
Description :
PTMCode is a resource of known and predicted functional associations between protein post-translational modifications (PTMs) within and between interacting proteins. It currently contains 316,546 modified sites from 69 different PTM types which are also propagated through ortholgs between 19 differe ...
Taxonomy : Eukaryota
Visit : http://ptmcode.embl.de/

Publication Information

Article : PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins
Author : Pablo Minguez, Ivica Letunic, Luca Parca1, Luz Garcia-Alonso, Joaquin Dopazo,Jaime Huerta-Cepas and Peer Bork1
Years : 2014
PubMed : 25361965

PTMfunc
Resource Type : DB
Description :
PTMfunc is a repository of functional predictions for protein post-translational modifications (PTMs). To find predictions for your protein of interest just search using a protein name or ID in the search box above. We rely mostly on ids from ENSEMBL but also have protein names for most species. For ...
Taxonomy : N/A
Visit : http://ptmfunc.com/

Publication Information

Article : Systematic functional prioritization of protein posttranslational modifications.
Author : Pedro Beltrao , Véronique Albanèse, Lillian R. Kenner, Danielle L. Swaney, Alma Burlingame, Judit Villén, Wendell A. Lim, James S. Fraser, Judith Frydman, Nevan J. Krogan
Years : 2012
PubMed : 22817900

PTM-SD
Resource Type : DB
Description :
Posttranslational modifications (PTMs) define covalent and chemical modifications of protein residues. They play important roles in modulating various biological functions. Current PTM databases contain important sequence annotations but do not provide informative 3D structural resource about these ...
Taxonomy : N/A
Visit : http://www.dsimb.inserm.fr/dsimb_tools/PTM-SD/

Publication Information

Article : PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.
Author : Pierrick Craveur, Joseph Rebehmed and Alexandre G. de Brevern
Years : 2014
PubMed : 24857970

PTM-X
Resource Type : Tool
Description :
Post-translational modification (PTM)(1) plays an important role in regulating the functions of proteins. PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM cross-talk. Identification of PTM cross-talks is an emerging theme in proteomi ...
Taxonomy : N/A
Visit : http://bioinfo.bjmu.edu.cn/ptm-x/

Publication Information

Article : Systematic characterization and prediction of post-translational modification cross-talk
Author : Huang Y, Xu B, Zhou X, Li Y, Lu M, Jiang R, Li T
Years : 2015
PubMed : 25605461

PyTMs
Resource Type : Tool
Description :
BACKGROUND: Post-translational modifications (PTMs) constitute a major aspect of protein biology, particularly signaling events. Conversely, several different pathophysiological PTMs are hallmarks of oxidative imbalance or inflammatory states and are strongly associated with pathogenesis of autoimmu ...
Taxonomy : N/A
Visit : http://www.pymolwiki.org/index.php/Pytms

Publication Information

Article : PyTMs: a useful PyMOL plugin for modeling common post-translational modifications.
Author : Andreas Warnecke, Tatyana Sandalova, Adnane Achour and Robert A Harris
Years : 2014
PubMed : 25431162

RedoxDB
Resource Type : DB
Description :
SUMMARY: Redox regulation and signaling, which are involved in various cellular processes, have become one of the research focuses in the past decade. Cysteine thiol groups are particularly susceptible to post-translational modification, and their reversible oxidation is of critical role in redox re ...
Taxonomy : N/A
Visit : http://biocomputer.bio.cuhk.edu.hk/RedoxDB/

Publication Information

Article : RedoxDB--a curated database for experimentally verified protein oxidative modification.
Author : Ming-an Sun, Yejun Wang, Han Cheng, Qing Zhang, Wei Ge and Dianjing Guo
Years : 2012
PubMed : 22833525

RESID
Resource Type : DB
Description :
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. ...
Taxonomy : N/A
Visit : http://pir.georgetown.edu/resid/

Publication Information

Article : The RESID Database of Protein Modifications: 2003 developments.
Author : John S. Garavelli
Years : 2003
PubMed : 12520062

SysPTM
Resource Type : DB
Description :
SysPTM Version 2.0, updated June 15th, 2013. Visits: 110. SysPTM provides a systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledge base of manually curated multi-type modification data, but also with four fully developed, in-depth data mining tools. ...
Taxonomy : N/A
Visit : http://lifecenter.sgst.cn/SysPTM/

Publication Information

Article : SysPTM 2.0: an updated systematic resource for post-translational modification.
Author : Jing Li, Jia Jia, Hong Li, Jian Yu, Han Sun, Ying He, Daqing Lv, Xiaojuan Yan2, Michael O. Glocker, Liangxiao Ma, Jiabei Yang, Ling Li, Wei Li, Guoqing Zhang, Qian Liu, Yixue Li and Lu Xie
Years : 2014
PubMed : 24705204

topPTM
Resource Type : DB
Description :
topPTM is a database that integrates experimentally verified post-translational modifications (PTMs) from available databases and research articles, and annotates the PTM sites on transmembrane proteins with structural topology. The biological effects of PTMs on transmembrane proteins include phosph ...
Taxonomy : N/A
Visit : http://topptm.cse.yzu.edu.tw/

Publication Information

Article : topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins.
Author : Min-Gang Su, Kai-Yao Huang, Cheng-Tsung Lu, Hui-Ju Kao, Ya-Han Chang and Tzong-Yi Lee
Years : 2014
PubMed : 24302577

BPB-PPMS
Resource Type : Tool
Description :
Protein methylation is one type of reversible post-translational modifications (PTMs), which plays vital roles in many cellular processes such as transcription activity, DNA repair. Experimental identification of methylation sites on proteins without prior knowledge is costly and time-consuming. In ...
Taxonomy : N/A
Visit : http://www.bioinfo.bio.cuhk.edu.hk/bpbpp?ms

Publication Information

Article : Computational Identification of Protein Methylation Sites through Bi-Profile Bayes Feature Extraction
Author : Jianlin Shao, Dong Xu, Sau-Na Tsai, Yifei Wang, Sai-Ming Ngai
Years : 2009
PubMed : 19290060

iMethyl-PseAAC
Resource Type : Tool
Description :
The web-server iMethyl-PseAAC is a web server that could predict methylation sites in proteins. With the assistance of SVM, the highlight of iMethyl-PseAAC is to employ amino acid sequence features extracted from the sequence evolution information via grey system model (Grey-PSSM). Caveat To obtain ...
Taxonomy : N/A
Visit : http://www.jci-bioinfo.cn/iMethyl-PseAAC

Publication Information

Article : iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach
Author : Wang-Ren Qiu, Xuan Xiao, Wei-Zhong Lin, and Kuo-Chen Chou
Years : 2014
PubMed : 24977164

MASA
Resource Type : Tool
Description :
Studies within the last few years have identified that protein methylation occurring on histones and other proteins are involved in the regulation of gene transcription. Several previous works were developed to computationally identify the potential methylation sites on lysine and arginine. With the ...
Taxonomy : N/A
Visit : http://MASA.mbc.nctu.edu.tw/

Publication Information

Article : Incorporating structural characteristics for identification of protein methylation sites.
Author : Dray-Ming Shien, Tzong-Yi Lee, Wen-Chi Chang, Justin Bo-Kai Hsu, Jorng-Tzong Horng, Po-Chiang Hsu, Ting-Yuan Wang andHsien-Da Huang
Years : 2009
PubMed : 19263424

MeMo
Resource Type : Tool
Description :
MeMo is the first protein methylation prediction server based on SVM (support vector machine). Limited by available training data, at present MeMo only focuses on Arginine and Lysine sites. Users could submit their protein sequences to predict which arginine and Lysine sites are undergoing methyla ...
Taxonomy : N/A
Visit : http://www.bioinfo.tsinghua.edu.cn/~tigerchen/memo.html

Publication Information

Article : MeMo: a web tool for prediction of protein methylation modifications.
Author : Hu Chen, Yu Xue, Ni Huang, Xuebiao Yao1 and Zhirong Sun
Years : 2006
PubMed : 16845004

PubMeth
Resource Type : DB
Description :
Epigenetics, and more specifically DNA methylation is a fast evolving research area. In almost every cancer type, each month new publications confirm the differentiated regulation of specific genes due to methylation and mention the discovery of novel methylation markers. Therefore, it would be extr ...
Taxonomy : Eukaryota, Animals
Visit : http://www.pubmeth.org

Publication Information

Article : PubMeth: a cancer methylation database combining text-mining and expert annotation.
Author : Maté Ongenaert, Leander Van Neste, Tim De Meyer, Gerben Menschaert, Sofie Bekaert and Wim Van Criekinge
Years : 2008
PubMed : 17932060

MYRbase
Resource Type : DB
Description :
Myristoylation is a common lipid modification of proteins in Eukaryotes and their Viruses as well as some Bacteria and essential for the function of several important proteins (such as G proteins, SRC and related kinases, ADP ribosylation factors, HIV gag, HIV nef,...). The saturated 14-carbon fatty ...
Taxonomy : Eukaryota
Visit : http://mendel.imp.ac.at/myristate/myrbase/

Publication Information

Article : MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins. Genome biology.
Author : Sebastian Maurer-Stroh, Masaki Gouda, Maria Novatchkova,Alexander Schleiffer, Georg Schneider, Fernanda L Sirota,Michael Wildpaner, Nobuhiro Hayashi and Frank Eisenhaber
Years : 2004
PubMed : 15003124

NMT
Resource Type : Tool
Description :
Many posttranslational modifications (N-myristoylation or glycosylphosphatidylinositol (GPI) lipid anchoring) and localization signals (the peroxisomal targeting signal PTS1) are encoded in short, partly compositionally biased regions at the N- or C-terminus of the protein sequence. These sequence s ...
Taxonomy : Eukaryota, Animals, Fungi
Visit : http://mendel.imp.ac.at/myristate/SUPLpredictor.htm

Publication Information

Article : Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1.
Author : Frank Eisenhaber, Birgit Eisenhaber, Werner Kubina, Sebastian Maurer-Stroh, Georg Neuberger, Georg Schneider and Michael Wildpaner
Years : 2003
PubMed : 12824382

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

PRENbase
Resource Type : DB
Description :
PRENbase is an annotated database of known and predicted prenylated proteins. Homologous proteins are merged into clusters. This search interface is designed to allow sophisticated queries for the experimental status of the modification (known/predicted...), exclusive or shared types of modifying en ...
Taxonomy : N/A
Visit : http://mendel.imp.ac.at/PrePS/PRENbase/

Publication Information

Article : Towards complete sets of farnesylated and geranylgeranylated proteins.
Author : Sebastian Maurer-Stroh , Manfred Koranda, Wolfgang Benetka, Georg Schneider, Fernanda L Sirota, Frank Eisenhaber
Years : 2007
PubMed : 17411337

PrePS
Resource Type : Tool
Description :
PrePS stands for Prenylation Prediction Suite and combines three predictors for protein CaaX farnesylation, CaaX geranylgeranylation and Rab geranylgeranylation in one webinterface. The predictors aim to model the substrate-enzyme interactions based on refinement of the recognition motifs for each o ...
Taxonomy : N/A
Visit :  http://mendel.imp.univie.ac.at/sat/PrePS

Publication Information

Article : Refinement and prediction of protein prenylation motifs.
Author : Sebastian Maurer-Stroh and Frank Eisenhaber
Years : 2005
PubMed : 15960807

GPS-PUP
Resource Type : Tool
Description :
The Nobel Prize in Chemistry 2004 was award to Aaron Ciechanover, Avram Hershko and Irwin Rose for their discovery of ubiquitin-mediated protein degradation. (Vogel, G. et al., 2004). Numerous subsequent studies showed that the selective degradation by ubiquitination provided a critical mechanism in ...
Taxonomy : Archaea, Bacteria
Visit : http://pup.biocuckoo.org/

Publication Information

Article : GPS-PUP: computational prediction of pupylation sites in prokaryotic proteins.
Author : Zexian Liu,Qian Ma,Jun Cao,Xinjiao Gao,Jian Ren and Yu Xue
Years : 2011
PubMed : 21850344

dbGSH
Resource Type : DB
Description :
dbGSH is a database that integrates the experimentally verified cysteine S-glutathionylation (GSH) sites from multiple species. S-glutathionylation (GSH), the reversible protein post-translational modification (PTM) that generates a mixed-disulfide bond between glutathione and cysteine reside, crit ...
Taxonomy : N/A
Visit : http://csb.cse.yzu.edu.tw/dbGSH/

Publication Information

Article : dbGSH: a database of S-glutathionylation.
Author : Yi-Ju Chen, Cheng-Tsung Lu, Tzong-Yi Lee, and Yu-Ju Chen
Years : 2014
PubMed : 24790154

GSTPred
Resource Type : Tool
Description :
GSTpred is a web-server specially trained for the Glutathione S-transferase protein.The prediction is based on the basis of amino acid composition, dipeptide composition, tripeptide composition by using support vector machines(SVM).The prediction result will be displayed on web browser in tabular fo ...
Taxonomy : N/A
Visit : http://www.imtech.res.in/raghava/gstpred/

Publication Information

Article : Support vector machine based prediction of glutathione S-transferase proteins.
Author : Nitish Kumar Mishra, Manish Kumar and G.P.S. Raghava
Years : 2007
PubMed : 17627599

dbSNO
Resource Type : DB
Description :
Protein S-nitrosylation (SNO) is a reversible post-translational modification (PTM) and involves the covalent attachment of nitric oxide (NO) to the thiol group of cysteine (Cys) residues. Given the increasing number of proteins reported to be regulated by this modification, S-nitrosylation is consi ...
Taxonomy : N/A
Visit : http://140.138.144.145/~dbSNO/index.php

Publication Information

Article : dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation.
Author : Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Kai-Yao Huang, Wei-Chieh Ching, Hsiao-Hsiang Yang, Yen-Chen Liao, Yu-Ju Chen and Tzong-Yi Lee
Years : 2014
PubMed : 25399423

GPS-SNO
Resource Type : Tool
Description :
The Nobel Prize in Chemistry 2004 was award to Aaron Ciechanover, Avram Hershko and Irwin Rose for their discovery of ubiquitin-mediated protein degradation. (Vogel, G. et al., 2004). Numerous subsequent studies showed that the selective degradation by ubiquitination provided a critical mechanism in ...
Taxonomy : N/A
Visit : http://sno.biocuckoo.org/

Publication Information

Article : GPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm.
Author : Yu Xue , Zexian Liu, Xinjiao Gao, Changjiang Jin, Longping Wen, Xuebiao Yao, Jian Ren
Years : 2010
PubMed : 20585580

iSNO-AAPair
Resource Type : Tool
Description :
The web-server iSNO-AAPair is established for predicting the cysteine S-nitrosylation sites in proteins. Caveats: 1.To obtain the predicted result with the anticipated success rate, the entire sequence of the query protein rather than its fragment should be used as an input. A sequence with less t ...
Taxonomy : N/A
Visit : http://app.aporc.org/iSNO-AAPair/index.html

Publication Information

Article : iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins.
Author : Yan Xu?, Xiao-Jian Shao, Ling-Yun Wu, Nai-Yang Deng, Kuo-Chen Chou?
Years : 2013
PubMed : 24109555

iSNO-PseAAC
Resource Type : Tool
Description :
The web-server iSNO-AAPair is established for predicting the cysteine S-nitrosylation sites in proteins. Caveats: 1.To obtain the predicted result with the anticipated success rate, the entire sequence of the query protein rather than its fragment should be used as an input. A sequence with less t ...
Taxonomy : N/A
Visit : http://app.aporc.org/iSNO-PseAAC/

Publication Information

Article : iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition.
Author : Yan Xu , Jun Ding, Ling-Yun Wu, Kuo-Chen Chou
Years : 2013
PubMed : 23409062

PSNO
Resource Type : Tool
Description :
S-nitrosylation (SNO) is one of the most universal reversible post-translational modifications involved in many biological processes. Malfunction or dysregulation of SNO leads to a series of severe diseases, such as developmental abnormalities and various diseases. Therefore, the identification of S ...
Taxonomy : N/A
Visit : http://59.73.198.144:8088/PSNO/

Publication Information

Article : PSNO: predicting cysteine S-nitrosylation sites by incorporating various sequence-derived features into the general form of Chou's PseAAC.
Author : Jian Zhang , Xiaowei Zhao , Pingping Sun and Zhiqiang Ma
Years : 2014
PubMed : 24968264

iSuc-PseAAC
Resource Type : Tool
Description :
The web-server iSNO-AAPair is established for predicting the cysteine S-nitrosylation sites in proteins. Caveats: 1.To obtain the predicted result with the anticipated success rate, the entire sequence of the query protein rather than its fragment should be used as an input. A sequence with less t ...
Taxonomy : N/A
Visit : http://app.aporc.org/iSuc-PseAAC/

Publication Information

Article : iSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity
Author : Yan Xu,Ya-Xin Ding,Jun Ding,Ya-Hui Lei,Ling-Yun Wu
Years : 2015
PubMed : 26084794

GPS-SUMO
Resource Type : Tool
Description :
The Nobel Prize in Chemistry 2004 was award to Aaron Ciechanover, Avram Hershko and Irwin Rose for their discovery of ubiquitin-mediated protein degradation. (Vogel, G. et al., 2004). Numerous subsequent studies showed that the selective degradation by ubiquitination provided a critical mechanism in ...
Taxonomy : N/A
Visit : http://sumosp.biocuckoo.org/

Publication Information

Article : GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs
Author : Qi Zhao, Yubin Xie, Yueyuan Zheng, Shuai Jiang, Wenzhong Liu, Weiping Mu,Zexian Liu, Yong Zhao, Yu Xue, and Jian Ren
Years : 2014
PubMed : 24880689

JASSA
Resource Type : Tool
Description :
SUMOylation is a post-translational modification conserved from yeast to human that modulates several fundamental cellular processes, and have been showed to be involved in human disorders. It consists of the covalent attachment of a small ubiquitin-related modifier protein (SUMO) to a target protei ...
Taxonomy : N/A
Visit : http://www.jassa.fr/

Publication Information

Article : JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs
Author : Guillaume Beauclair, Antoine Bridier-Nahmias, Jean-François Zagury, Ali Saïb, Alessia Zamborlini
Years : 2015
PubMed : 26142185

SUMOhydro
Resource Type : Tool
Description :
SUMOhydro has been developed to predict sumoylation lysine (K) sites in proteins by introduction of hydrophobicity to binary encoding. With the assistance of Support Vector Machine (SVM)(http://svmlight.joachims.org/), the predictor was trained and tested in a new and stringent sumoylation sites dat ...
Taxonomy : N/A
Visit : http://protein.cau.edu.cn/others/SUMOhydro/introduction.html

Publication Information

Article : SUMOhydro: a novel method for the prediction of sumoylation sites based on hydrophobic properties
Author : Yong-Zi Chen, Zhen Chen, Yu-Ai Gong, Guoguang Ying
Years : 2012
PubMed : 22720073

SUMOplot
Resource Type : Tool
Description :
The SUMOplot™ Analysis Program predicts and scores sumoylation sites in your protein. The presence of this post-translational modification may help explain larger MWs than expected on SDS gels due to attachment of SUMO protein (11kDa) at multiple positions in your protein. SUMO-1 (small ubiquitin-r ...
Taxonomy : N/A
Visit : http://www.abgent.com/sumoplot

Publication Information

Article :
Author :
Years :
PubMed :

The Sulfinator
Resource Type : Tool
Description :
The Sulfinator is a software tool able to predict tyrosine sulfation sites in protein sequences. It employs four different Hidden Markov Models that were built to recognise sulfated tyrosine residues located N-terminally, within sequence windows of more than 25 amino acids and C-terminally, as well ...
Taxonomy : N/A
Visit : http://web.expasy.org/sulfinator/

Publication Information

Article : The Sulfinator: predicting tyrosine sulfation sites in protein sequences.
Author : Monigatti F, Gasteiger E,Bairoch A, Jung E.
Years : 2002
PubMed : 12050077

hCKSAAP_UbSite
Resource Type : Tool
Description :
CKSAAP_UbSite is a web server that could predict ubiquitination sites in proteins. With the assistance of SVM, the highlight of CKSAAP_UbSite is to employ the composition of k-spaced amino acid pairs as input feature vector. It was trained and tested on a set of experimentally verified ubiquitinatio ...
Taxonomy : N/A
Visit : http://protein.cau.edu.cn/cksaap_ubsite/

Publication Information

Article : hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
Author : Zhen Chena,Yuan Zhoua,Jiangning Songb,Ziding Zhanga
Years : 2013
PubMed : 23603789

iUbiq-Lys
Resource Type : Tool
Description :
The web-server iUbiq-Lys is a web server that could predict ubiquitination sites in proteins. With the assistance of SVM, the highlight of iUbiq-Lys is to employ amino acid sequence features extracted from the sequence evolution information via grey system model (Grey-PSSM). ...
Taxonomy : N/A
Visit : http://www.jci-bioinfo.cn/iUbiq-Lys

Publication Information

Article : iUbiq-Lys: prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model.
Author : Wang-Ren Qiua, Xuan Xiao, Wei-Zhong Lina & Kuo-Chen Choucd
Years : 2015
PubMed : 25248923

UbiPred
Resource Type : Tool
Description :
BACKGROUND: Ubiquitylation plays an important role in regulating protein functions. Recently, experimental methods were developed toward effective identification of ubiquitylation sites. To efficiently explore more undiscovered ubiquitylation sites, this study aims to develop an accurate sequence-ba ...
Taxonomy : N/A
Visit : http://iclab.life.nctu.edu.tw/ubipred

Publication Information

Article : Computational identification of ubiquitylation sites from protein sequences.
Author : Chun-Wei Tung and Shinn-Ying Ho
Years : 2008
PubMed : 18625080

UbiProber
Resource Type : Tool
Description :
Systematic dissection of the ubiquitylation proteome is emerging as an appealing but challenging research topic because of the significant roles ubiquitylation plays not only in protein degradation but also in many other cellular functions. Since ubiquitylation is rapid and reversible, it is time-co ...
Taxonomy : N/A
Visit : http://bioinfo.ncu.edu.cn/UbiProber.aspx

Publication Information

Article : Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites.
Author : Xiang Chen, Jian-Ding Qiu, Shao-Ping Shi,Sheng-Bao Suo, Shu-Yun Huang and Ru-Ping Liang
Years : 2013
PubMed : 23626001

UbPred
Resource Type : Tool
Description :
UbPred is a random forest-based predictor of potential ubiquitination sites in proteins. It was trained on a combined set of 266 non-redundant experimentally verified ubiquitination sites available from our experiments and from two large-scale proteomics studies (Hitchcock, et al., 2003; Peng, et al ...
Taxonomy : N/A
Visit : http://www.ubpred.org/

Publication Information

Article : Identification, analysis, and prediction of protein ubiquitination sites.
Author : Predrag Radivojac, Vladimir Vacic, Chad Haynes, Ross R. Cocklin, Amrita Mohan, Joshua W. Heyen, Mark G. Goebl andLilia M. Iakoucheva
Years : 2010
PubMed : 19722269

UbiProt
Resource Type : DB
Description :
The UbiProt Database project aims to summarize a significant volume of data concerning various protein substrates of ubiquitylation. Each database entry describing particular ubiquitylated protein comprises information about protein properties and sources; ubiquitylation features, including details ...
Taxonomy : N/A
Visit : http://ubiprot.org.ru/

Publication Information

Article : UbiProt: a database of ubiquitylated proteins.
Author : Alexander L Chernorudskiy, Alejandro Garcia, Eugene V Eremin, Anastasia S Shorina, Ekaterina V Kondratieva and Murat R Gainullin
Years : 2007
PubMed : 17442109