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 data. Motif-x can extract over-represented patterns from any sequence data set. It permits users to import their data and also to download results that use Web browsers on essentially any Web-compatible computer.
Simplifies the recognition of large sets of spectra and improves the flexibility of post-translational modification (PTM) searching. DBDigger is implemented for single-pass, rapid scoring of potential matches. The software discovers peptides from multiple isotopic distributions in a single pass. It automates the determination of the mass for each amino acid residue based on the specified isotopic distributions.
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 analysis tools (PTMBlast, PTMPathway, PTMPhylog, PTMCluster). The multi-organism feature of this application makes it extremely useful for comparative modificomics. Additionally, multi-site and multi-type modification can be investigated.
Allows users to develop systematic searches for proteins of interest and explore network visualisations that address complex post-translational modifications of proteins (PTM)-associated relationships. PTMOracle is a Cytoscape app for co-analysing PTMs within protein-protein interaction (PPI) networks. It also allows extensive data to be integrated and co-analysed with PPI networks, allowing the role of domains, motifs and disordered regions to be considered. For proteins of interest, or a whole proteome, PTMOracle can generate network visualisations to reveal complex PTM-associated relationships.
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 engines. ModLS can also perform localization scoring for any PTM selected as a variable modification in a search, from those defined in the comprehensive UniMod database. ModLS is part of the Central Proteomics Facilities Pipeline.
Predicts whether sites of protein modifications are inside or outside of protein-protein interacting regions (PPIRs), based on the existing structural and post-translational modifications (PTM) databases. PtmPPIR showed high performance measures, and important features contributing to predictive power were identified. The models were evaluated using 10 independent iterations of 5-fold cross-validation, and the resulting calculated performance measures for the models were high.
Enables identification of peptide modifications. Comet-PTM is an engine that takes account of the mass shift produced by the modification in the fragmentation series, producing the same score as a conventional “closed” searches (CS) using the same mass increment as a variable modification. It resolves the modification mass shift in the fragmentation series, doubling the number of modified peptides identified by conventional OS and matching the identification performance of targeted CS.
Aims to ensure the transparency and reproducibility of data analysis process and results. MS-PyCloud is a cloud computing-based pipeline for liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) data analysis. This method includes three major components: (i) peptide identification through database search, (ii) protein inference and (iii) protein or post-translational modifications (PTMs) quantitation.
Identifies protein post-translational modification (PTM) motifs. MoMo is a web server, integrated into the MEME Suite, that performs motif discovery in peptide sequences using one of three algorithms: motif-x, MoDL or simple alignment. The software can discover in a single run separate motifs for each combination of amino acid residue and modification mass, or report a single motif for each modification mass. It is also able to read peptide spectrum match (PSM) output formats from popular mass spectrometry search engine.
Predicts modification sites across the proteome. PTMscape uses a unified set of descriptors of the physico-chemical microenvironment of modified sites to process. It constructs sub-sequence windows centered at known or candidate post-translational modification (PTM) sites. This software features statistical tests for the enrichment of protein domains in individual PTM sites and enables the annotation of the prediction output with domain and sub-cellular information.
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 fingerprinting results of known proteins for the presence of 22 types of PTMs of discrete mass.
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 regions, termed extein, ligate to form a mature protein. This server is an attempt to help biolgist identify Inteins hiding in their protein sequences.
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 bioinformatics tools, chemistry tools and to or from mass spectrometry (MS) instruments.
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 well as structures similarity searches added to options filters such as the possibility of finding tautomers for structure. It includes both a free and a licensed version. The free version only allows users to open a limited number of links.
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