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Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques.
Compare amino acid composition of a UniProtKB entry with some or all other UniProtKB entries. Several constellations are available, corresponding to various amino acid analysis techniques.
Digitized version of the Roche Applied Science "Biochemical Pathways" wall chart. The map, linked to relevant ENZYME database entries, can be browsed online, and keyword searches are available.
BLAST sequence similarity search (blastp or tblastn) against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB, EMBL, ESTs
keywords: similarity search
Compute the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of UniProt Knowledgebase (Swiss-Prot or TrEMBL) entries or for user entered sequences
Redundancy reduction in a set of aligned or unaligned sequences
ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
Predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides. The experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot/TrEMBL entry or from a user-entered sequence, and mass differences are used to better characterise the protein of interest.
Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage.
Calculate the mass of an oligosaccharide structure.
Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides.
GPSDB (Gene and Protein Synonym DataBase) collects gene/protein names, in a species specific way, from several biological resources. A web-based search interface gives access to the database: given a gene/protein name, it retrieves all synonyms for this entity and queries Medline with a set of user-selected terms.
HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
Scan several sequences or a whole genome (all ORFs) against the HAMAP families, with partial or complete annotation in UniProtKB/Swiss-Prot format.
A tool to merge the peptide sequence-ion m/z range from CID spectra and the reporter-ion m/z range from HCD spectra into the appropriate single file, to be further used in identification and quantification search engines
Melanie offers a unique and flexible interface for the comprehensive visualization, exploration and analysis of 2D gel data. It provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE (Fluorescence Difference Gel Electrophoresis) gels.
Isotopident can estimate the theoretical isotopic distribution of a peptide or protein, a polynucleotide and a chemical compound from its composition (sequence of amino acids expressed in either 1-letter code, sequence of amino acids expressed in 3-letter code, sequence of nucleotides or its chemical formula). Isotopident can also compute its monoisotopic mass. and predict the most likely isotope combination and the exact mass of the given input.
Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. The tool offers the possibility to automatically update data related to numerous external data resources. It is also possible to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. This tool can also be used to build up 2D-PAGE repositories, accessible by any one from the Web.
A tool to quantify MALDI peptides (SILAC) from Phenyx output
MIAPEGelDB helps end-users to write MIAPE documents (minimum information to report when describing or publishing a proteomics experiment), through a self-documenting web interface. The produced documents are stored in a database, and thus remain easily accessible by anybody through a stable URL unique for each document.
keywords: gel electrophoresis, protocol