Provides a central, user-friendly knowledgebase that integrates data on protein termini, their modifications and information on underlying proteolytic processes extracted from existing valuable resources and make this combined information accessible to a broad audience. TopFIND is designed as non-redundant, protein centric database. Each protein is represented by its genomic encoded polypeptide sequence and further detailed by general annotation such as alternative protein names, protein function and role in disease and by sequence-specific annotation as isoforms, domains and sequence variants. In addition to these commonly assembled protein characteristics TopFIND catalogs detailed information on protein chains, termini, modifications of the terminal amino acid and proteolytic processes.
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.
Provides information about protein post-translational modifications (PTMs) and protein annotations. ProteomeScout allows the community to deposit PTM experiments. It offers a way to explore and analyze PTM experiments. This tool contains data such as Gene Ontology (GO) annotations, domains, secondary structure and non-synonymous polymorphisms. It also provides analysis tools for experimental datasets.
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 automatically load the new PTM IDs, curate them, and quantify and even categorize by organism this information every month as the Swiss-Prot Knowledgebase is updated. PTMCurator was created with the intention of being used at-large as a continuously updated resource for use by the academic community.
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 the peptide spectrum matches, sequence coverage information, or tandem mass spectrometry (MS/MS) spectra and extracted ion chromatograms through a single. It allows easy and comprehensive visualization of small and medium bottom-up proteomics datasets.
Serves for molecular modelling studies and QSAR analysis. BISSCat is an online resource containing a lot of functional groups (over 400), compounds (more than 200 000), and computationally constructed substructures (about 1 000 000). It is useful to search functional groups and compounds. It provides several information to assists users in determination of substrates for known enzymes or putative enzymes.
Gathers information about post-translational modifications (PTMs). MPTMDB is an online resource that covers target proteins, enzymes, sites, organisms and human diseases related to PTM. It enables versatile visualization of PTMs, substrates and interacting enzymes.
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 discovery, connecting enzyme-substrate relationships, major PTMs that may work in concert, PTM forms to biological contexts and across taxons. This database allows users to search, browse, review results interactively, visualize PTM in protein networks and pathway maps, conduct use cases.