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Open AccessJournal ArticleDOI

Activities at the Universal Protein Resource (UniProt)

Rolf Apweiler, +133 more
TLDR
The mission of the Universal Protein Resource (UniProt) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation.
Abstract
The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation. It integrates, interprets and standardizes data from literature and numerous resources to achieve the most comprehensive catalog possible of protein information. The central activities are the biocuration of the UniProt Knowledgebase and the dissemination of these data through our Web site and web services. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.

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Citations
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IthaGenes: an interactive database for haemoglobin variations and epidemiology.

TL;DR: IthaGenes is a new interactive database of haemoglobin variations, which stores information about genes and variations affecting ha Hemoglobin disorders, while embedding the NCBI Sequence Viewer for graphical representation of each variation.
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CPLM: a database of protein lysine modifications

TL;DR: The various PLM crosstalks suggested that a considerable proportion of lysines were competitively and dynamically regulated in a complicated manner and can serve as a useful resource for further research of PLMs.
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Conserved mRNA-binding proteomes in eukaryotic organisms.

TL;DR: The repertoire of 765 and 594 proteins that reproducibly interact with polyadenylated mRNAs in Saccharomyces cerevisiae and Caenorhabditis elegans are described and it is speculated that enzyme-mRNA interactions relate to an ancient mechanism for post-transcriptional coordination of metabolic pathways that perhaps was established during the transition from the early 'RNA world' to the 'protein world'.
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Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses.

TL;DR: Unexpected sequence cooperativity consequences were revealed by PICS that uniquely encompasses both the non-prime and prime sides flanking the proteomic-pinpointed scissile bond, cementing the conclusion that non- prime side flexibility greatly impacts MMP binding affinity and cleavage efficiency.
References
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Journal ArticleDOI

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

TL;DR: The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides a non-redundant collection of sequences representing genomic data, transcripts and proteins that pragmatically includes sequence data that are currently publicly available in the archival databases.
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COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.

TL;DR: With all genomic information recently updated to GRCh37, COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.
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Saccharomyces Genome Database: the genomics resource of budding yeast

TL;DR: The Saccharomyces Genome Database is an encyclopedia of the yeast genome, its chromosomal features, their functions and interactions, and public access to these data is provided to researchers and educators via web pages designed for optimal ease of use.
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UniRef: comprehensive and non-redundant UniProt reference clusters.

TL;DR: The UniRef (UniProt Reference Clusters) provides clustered sets of sequences from the UniProt Knowledgebase and selected UniProt Archive records to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences.
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