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Other software tools | Post-translational modification analysis

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…

PTMfunc
Dataset

PTMfunc

A repository of functional predictions for protein post-translational…

A repository of functional predictions for protein post-translational modifications (PTMs).

dbPTM
Dataset

dbPTM

An integrated resource for post-translational modifications (PTMs), providing…

An integrated resource for post-translational modifications (PTMs), providing not only a comprehensive dataset of experimentally verified PTMs that are supported by the literature but also an…

HIstome
Dataset

HIstome

A database of human histones, their post-translational modifications and…

A database of human histones, their post-translational modifications and modifying enzymes. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes…

TopFIND
Dataset

TopFIND Terminus Oriented Protein Function Inferred Database

Provides a central, user-friendly knowledgebase that integrates data on protein…

Provides a central, user-friendly knowledgebase that integrates data on protein termini, their modifications and information on underlying proteolytic processes extracted from existing valuable…

MsViz
Dataset

MsViz

Supports manual validation of post-translational modifications (PTMs) and their…

Supports manual validation of post-translational modifications (PTMs) and their relative quantitation in small- and medium-size experiments. MsViz can display thanks to its interactive interface with…

PLMD
Dataset

PLMD Protein Lysine Modification Database

Enables to browse on a data resource of protein lysine modification database.…

Enables to browse on a data resource of protein lysine modification database. PLMD allows users to search through an interface containing more than 280 000 modifications events in more than 53 000…

ProP
Web

ProP

Predicts arginine and lysine propeptide cleavage sites in eukaryotic protein…

Predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks.

DSDBASE
Dataset

DSDBASE

A database on disulphide bonds in proteins that provides information on native…

A database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein.

NetPicoRNA
Web

NetPicoRNA

Produces neural network predictions of cleavage sites of picornaviral proteases.

Produces neural network predictions of cleavage sites of picornaviral proteases.

RESID
Dataset

RESID

Stores annotations and structures for protein pre-, co- and post-translational…

Stores annotations and structures for protein pre-, co- and post-translational modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link modifications. RESID provides…

ProteomeScout
Dataset

ProteomeScout

A resource for the study of proteins and their post-translational modifications…

A resource for the study of proteins and their post-translational modifications (PTMs) consisting of a database of PTMs, a repository for experimental data, an analysis suite for PTM experiments, and…

NetGlycate
Web

NetGlycate

Predicts glycation of ε amino groups of lysines in mammalian proteins.…

Predicts glycation of ε amino groups of lysines in mammalian proteins. NetGlycate combines 60 artificial neural networks in a balloting procedure. It can be used by researchers to select relevant…

topPTM
Dataset

topPTM

A database that integrates experimentally verified post-translational…

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…

OccupancyMS
Desktop

OccupancyMS

Calculates the site stoichiometry of a phospho-sites measured under multiple…

Calculates the site stoichiometry of a phospho-sites measured under multiple conditions with quantitative mass spectrometry (MS). OccupancyMS is a MATLAB algorithm that provides confidence intervals.…

PrAS
Desktop

PrAS Prediction of Amidation Sites

Predicts amidation sites. PrAS is based on a Support Vector Machine (SVM)…

Predicts amidation sites. PrAS is based on a Support Vector Machine (SVM) method. It extracts information of position-based features, physicochemical and biochemical properties feature, predicted…

iPTMnet
Dataset

iPTMnet

Generates training sets for Post-translational modification (PTM) site…

Generates training sets for Post-translational modification (PTM) site prediction methods. iPTMnet is an online resource that aims to develop an integrative bioinformatics framework for PTM…

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…

NetCorona
Web

NetCorona

Prediction of Coronavirus 3CL Proteinase cleavage sites on amino acid sequences.

Prediction of Coronavirus 3CL Proteinase cleavage sites on amino acid sequences.

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…

NGOME
Web

NGOME

An algorithm for the prediction of spontaneous non-enzymatic deamidation of…

An algorithm for the prediction of spontaneous non-enzymatic deamidation of internal asparagine residues in proteins. Asparagine deamidation is modulated by protein local sequence, secondary…

CleavePred
Web

CleavePred

A web tool for predicting the cleavage sites of proproteins such as prohormones…

A web tool for predicting the cleavage sites of proproteins such as prohormones and neuropeptides. CleavePred's algorithm is powered by ASAP, a Machine-Learning framework for predicting local…

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
PyTMs
Desktop

PyTMs

A plugin implemented with the commonly used visualization software PyMOL. PyTMs…

A plugin implemented with the commonly used visualization software PyMOL. PyTMs enables users to introduce a set of common post-translational modifications (PTMs) into protein/peptide models and can…

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…

PTM-SD
Dataset
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,…

PTMCurator
Dataset

PTMCurator

An automated computational method for quantifying the number of each…

An automated computational method for quantifying the number of each post-translational modification reported experimentally and non-experimentally in the Swiss-Prot Knowledgebase. PTMCurator will…

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…

PeptideMap
Web

PeptideMap

A tool for finding modifications on polypeptide sequences. The modifications…

A tool for finding modifications on polypeptide sequences. The modifications can be affecting single amino acids (e.g. phosphorylation or oxidation) or cross-linking two amino acids (e.g. disulfide…

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.

PtmPPIR
Desktop
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…

Motifs tree
Web

Motifs tree

Predictors for initiator methionine cleavage (IMC) and Nα-terminal acetylation…

Predictors for initiator methionine cleavage (IMC) and Nα-terminal acetylation (N-Ac).

SysPTM
Web

SysPTM

Provides a systematic and sophisticated platform for proteomic PTM research,…

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…

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