PTM Related Resources

PTM : Meta        Type : Tool

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

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

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

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