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Other software tools | Post-translational modification analysis

Motif-x
Web

Motif-x motif extractor

Allows users to extract significant motifs from large data sets, like groups of…

Allows users to extract significant motifs from large data sets, like groups of proteins that share a common biological function and tandem mass spectrometry (MS/MS) post-translational modification…

Perseus
Desktop

Perseus

Aims to proteomics data analyses. Perseus extracts biologically meaningful…

Aims to proteomics data analyses. Perseus extracts biologically meaningful information from processed raw files. It uses bioinformatic analyses from MaxQuant output and completes the proteomics…

NformPred
Web

NformPred

Predicts N-terminal formylation sites from protein sequences using composition…

Predicts N-terminal formylation sites from protein sequences using composition of k-spaced amino acid pairs (CKSAAP) feature and Support Vector Machine (SVM) algorithm. NformPred is a web predictor…

PtmPPIR
Desktop
ProSeek
Web

ProSeek

Predicts prokaryotic propionylation site. ProSeek combines evolutionary…

Predicts prokaryotic propionylation site. ProSeek combines evolutionary information, sequenced derived information and predicted structural information of 1953 propionylation sites in 856 proteins.…

MPTM
Web
Desktop

MPTM Mining Protein Post-Translational Modifications

Extracts and organizes comprehensive post-translational modifications (PTMs)…

Extracts and organizes comprehensive post-translational modifications (PTMs) information from literature in PubMed. MPTM provides literature mining service for hydroxylation, myristoylation. It…

PTMOracle
Desktop

PTMOracle

Allows users to develop systematic searches for proteins of interest and…

Allows users to develop systematic searches for proteins of interest and explore network visualisations that address complex post-translational modifications of proteins (PTM)-associated…

ASAP
Desktop

ASAP Amino-acid Sequence Annotation Prediction

A universal machine learning (ML) framework for residue-level predictions. ASAP…

A universal machine learning (ML) framework for residue-level predictions. ASAP extracts efficiently and fast large set of window-based features from raw sequences. The platform also supports easy…

NetCGlyc
Web
Desktop

NetCGlyc

Produces neural network predictions of C-mannosylation sites in mammalian…

Produces neural network predictions of C-mannosylation sites in mammalian proteins. NetCGlyc correctly predicts 93% of both positive and negative C-mannosylation sites. The method was used to scan…

ADPRtool
Algorithm

ADPRtool

Predicts Asp-ADP-Ribosylation sites from human proteins. ADPRtool is based on…

Predicts Asp-ADP-Ribosylation sites from human proteins. ADPRtool is based on weighted support vector machine (WSVM), minimum redundancy maximum relevance (mRMR) and incremental feature selection…

PEIMAN
Desktop
SysPTM
Web

SysPTM

Provides a systematic and sophisticated platform for proteomic…

Provides a systematic and sophisticated platform for proteomic post-translational modifications (PTMs) research. SysPTM is a systematic resource for PTM research consisting of a PTM database and four…

TI2BioP
Desktop

TI2BioP Topological Indices to BioPolymers

A software uses for the calculation of spectral moments. TI2BioP is a tool that…

A software uses for the calculation of spectral moments. TI2BioP is a tool that combined homology-search methods with an alignment-free tool that uses protein four-color-maps. It allows mainly the…

FindMod
Web

FindMod

Allows prediction of potential protein post-translational modifications (PTMs).…

Allows prediction of potential protein post-translational modifications (PTMs). FindMod is able to retrieve potential single amino acid substitutions in peptides. It can analyze peptide mass…

ModLS
Desktop

ModLS

Supports localization of Post-Translational Modifications (PTMs) results from…

Supports localization of Post-Translational Modifications (PTMs) results from multiple search engines. ModLS is a method that operates on meta-search results combining output from these search…

Proteax
Web
Desktop

Proteax

Permits to handle proteins that are modified or derivate. Proteax allows to…

Permits to handle proteins that are modified or derivate. Proteax allows to interact with post-translationally and chemically modified protein sequences. It facilitates the transfer of data to…

Carboxylator
Web

Carboxylator

Identifies carboxylated proteins with modification sites in order to…

Identifies carboxylated proteins with modification sites in order to investigate the biological functions of carboxylated proteins. Users can submit their uncharacterized protein sequences, then,…

GSTPred
Desktop
Web

GSTPred

A web-server specially trained for the Glutathione S-transferase protein. The…

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…

ISSPred
Desktop
Web

ISSPred Intein Splice Site Prediction

Protein splicing is a recently discovered Post-translational Modification in…

Protein splicing is a recently discovered Post-translational Modification in which one internal fragment, termed intein (Protein introns), is excised from a precursor protein and the flanking…

CYSREDOX
Web

CYSREDOX

Predicting the redox state of cysteins in proteins from multiple sequence…

Predicting the redox state of cysteins in proteins from multiple sequence alignments.

PGluS
Web

PGluS

Identifies S-glutathionylated sites from primary protein sequences. PGluS can…

Identifies S-glutathionylated sites from primary protein sequences. PGluS can mine the protein information by using multiple features. In order to reduce the computational time, 5-fold cross…

CWM Global…
Web

CWM Global Search

Provides a platform allowing the retrieval of chemical structures by submitting…

Provides a platform allowing the retrieval of chemical structures by submitting plain three letter sequences codes. CWM Global Search is a web application able to perform substructures searches as…

MAP Kinase analyser
Desktop

MAP Kinase analyser Mitogen Activated Protein Kinase

Identifies P-Site, phosphorylation site consensus sequences and domain of the…

Identifies P-Site, phosphorylation site consensus sequences and domain of the Mitogen Activated Protein Kinase (MAPK) in plant genome. MAP Kinase analyser can recognize if the given protein sequence…

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