Databases

• UniProtKB • functional information on proteins • [more]
  UniProtKB  •  The UniProt Knowledgebase (UniProtKB) is produced by the UniProt consortium composed of EBI (Rolf Apweiler), PIR (Cathy Wu) and SIB (Swiss-Prot group, Ioannis Xenarios). It is the central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (manually-annotated records and curator-evaluated computational analysis) and UniProtKB/TrEMBL (computationally analyzed records awaiting manual annotation). [less]
• UniProtKB/Swiss-Prot • protein sequence database • [more]
  UniProtKB/Swiss-Prot  •  UniProtKB/Swiss-Prot is the manually annotated component of UniProtKB. It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis. [less]
• neXtProt • human proteins • [more]
  neXtProt  •  neXtProt is an innovative knowledge platform dedicated to human proteins. This resource contains a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt is continuously extended so as to provide many more carefully selected data sets and analysis tools. [less]

• ENZYME • enzyme nomenclature • [more]
  ENZYME  •  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. [less]
• GPSDB • gene and protein synonyms • [more]
  GPSDB  •  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. [less]
• HAMAP • Microbial proteome annotation in UniProtKB • [more]
  HAMAP  •  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. [less]
• UniPathway • metabolic pathways for the UniProtKB • [more]
  UniPathway  •  UniPathway is a curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. [less]

Tools

• AACompSim • amino acid composition comparison • [more]
  AACompSim  •  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. [less]
• Biochemical Pathways • Biochemical Pathways • [more]
  Biochemical Pathways  •  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. [less]
• Compute pI/MW • theoretical pI and Mw computation • [more]
  Compute pI/MW  •  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 [less]
• FindMod • protein post-translational modification prediction • [more]
  FindMod  •  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. [less]
• FindPept • peptide identification from unspecific cleavage • [more]
  FindPept  •  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. [less]
• HAMAP • Microbial proteome annotation in UniProtKB • [more]
  HAMAP  •  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. [less]
• IsotopIdent • theoretical isotopic distribution • [more]
  IsotopIdent  •  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.  [less]
• ProtParam • protein physical and chemical parameters • [more]
  ProtParam  •  Compute various physical and chemical parameters for a given protein sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY). [less]
• ProtScale • protein profile computation and representation • [more]
  ProtScale  •  Compute and represent the profile produced by any amino acid scale on a selected protein sequence. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but ProtScale provides more than 50 predefined scales entered from the literature. [less]