UniProt Knowledgebase: a hub of integrated protein data

By Michele Magrane. Database J. Biol. Databases Curation, 2011

1,581 citations recorded by the source corpus.

The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialized data collections. UniProtKB also integrates a range of data from other resources. All information is attributed to its original source, allowing users to trace the provenance of all data. The UniProt Consortium is committed to using and promoting common data exchange formats and technologies, and UniProtKB data is made freely available in a range of formats to facilitate integration with other databases. Database URL: http://www.uniprot.org/

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/b766885b3486b7156e538f1de9d6603a5a197a10

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Citations in the corpus

Topology Prediction of α-Helical Transmembrane Proteins (2016, background): “The most important source for protein sequences used in my work is the UniProt Knowledgebase (UniProtKB) [45].”
PredictProtein—an open resource for online prediction of protein structural and functional features (2014, positive): “Database searches: sequences similar to the query are identified by standard, pairwise BLAST (8) and iterated PSI-BLAST (7) searches (9,10) against a non-redundant combination of PDB (11), Swiss-Prot (12) and TrEMBL (1).”
Database resources of the National Center for Biotechnology Information (2014, methodology): “In addition to these GenPept sequences, the Protein database also contains sequences from TPA, UniProtKB/SwissProt (38), the Protein Research Foundation (PRF) and the Protein Data Bank (PDB) (39).”
The BioPlex Network: A Systematic Exploration of the Human Interactome (2015, positive): “, 1994), spectra were searched against human protein sequences from Uniprot (Magrane and Consortium, 2011) and common contaminants.”
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 (2012, methodology): “To facilitate access to this information, our PubChem cross-references, along with other automatically aggregated cross-references to resources such as UniProt (25), IntAct (26) and SABIO-RK (27), are available on the ‘Automatic Xrefs’ tab of the ChEBI web display and are updated with every monthly ”
Tissue-based map of the human proteome (2015, methodology): “We have determined the number of genes for which evidence is available at a protein level by combining our antibody-based data with the manual annotation of literature by the UniProt consortium (5) and the results from the recent mass spectrometry–based proteogenomics analyses (9, 10, 12).”
Pi-Pi contacts are an overlooked protein feature relevant to phase separation (2018, methodology): “Phase separation critical concentration values for the N-terminus (1-236) of human Ddx4 and three mutants, 9FtoA and 14FtoA, as reported in (14), and RtoK, where all arginine residues have been mutated to lysine, as well as for the C-terminus (445-632) of human FMR1 and one mutant with all arginine ”