neXtProt

[…] riety of non-overlapping information, including PTMs and disease mutations. In addition to the comprehensive protein resource, UniProt, there are resources that specialize in specific species such as neXtProt for human and the Mouse Genome Informatics (MGI) for mouse. The Protein Ontology (PRO) and iPTMnet capture specific data types on proteoforms and post-translational modifications (PTMs), resp […]

[…] phical sequence output highlighting the position of the alpha repeats within the candidate exchanger, and also a chart depicting residue frequency. The sequence graphical output was modified from the neXtProt protein sequence viewer available at biojs.io, and the chart is generated using a JavaScript function to convert the residue frequency into a JSON object for canvas.js (https://canvasjs.com/) […]

[…] untries [].At the beginning of the C-HPP there were established resources on proteomic MS-data (PRIDE [], GPMdb [] and PeptideAtlas []); affinity data (Human Protein Atlas []); human proteome data in neXtProt []; and flexible platforms to work with heterogeneous molecular data, such as TAVERNA []. Despite such a representative diversity of existing IT-frameworks, new systems were launched: The Pro […]

[…] The datasets were analyzed following the HUPO Guidelines for the identification of proteins using MS/MS experiments. We searched all the mgf files obtained against the neXtProt database (release 20160111) [] using the target-decoy strategy with an in-house Mascot Server v. 2.3 (Matrix Science, London, UK) search engine. Decoy database was created using the peptide p […]

[…] nce, absence of expression in a given tissue, expression only in rare samples, and unfavorable structure (or cleavage sites) for MS studies such as instability or heterogeneity [, ]. Furthermore, the neXtProt is utilized as the reference database for the annotation of human proteins in the beginning period of the C-HPP [, ]. This database assigns experimental evidence to each human protein using a […]

[…] veral other biological databases and online platforms which allows the users of these external resources to gain further knowledge about enzymatic activities of enzymes (links from UniProtKB, BRENDA, NextProt (), ChloroKB (), MetaCrop) and detailed information about kinetics of biochemical reactions (links from KEGG Reaction, MetaNetX (), BKMS-react ()) as well as the participation and meaning of […]