Activities at the Universal Protein Resource (UniProt)
Rolf Apweiler,Alex Bateman,Maria Jesus Martin,Claire O'Donovan,Michele Magrane,Yasmin Alam-Faruque,Emanuele Alpi,Ricardo Antunes,J Arganiska,EB Casanova,Benoit Bely,M Bingley,Carlos Bonilla,Ramona Britto,Borisas Bursteinas,WM Chan,Gayatri Chavali,Elena Cibrian-Uhalte,A Da Silva,M De Giorgi,Tunca Doğan,F. Fazzini,Paul Gane,Leyla Jael Garcia Castro,Penelope Garmiri,Emma Hatton-Ellis,Reija Hieta,Rachael P. Huntley,Duncan Legge,W Liu,Jie Luo,Alistair MacDougall,Prudence Mutowo,Andrew Nightingale,Sandra Orchard,Klemens Pichler,Diego Poggioli,Sangya Pundir,L Pureza,Guoying Qi,S. Rosanoff,Rabie Saidi,Tony Sawford,Aleksandra Shypitsyna,Edd Turner,Volynkin,Tony Wardell,Xavier Watkins,Hermann Zellner,Matthew Corbett,M Donnelly,P van Rensburg,Mickael Goujon,Hamish McWilliam,Rodrigo Lopez,Ioannis Xenarios,Lydie Bougueleret,Alan Bridge,Sylvain Poux,Nicole Redaschi,Lucila Aimo,Andrea H. Auchincloss,Kristian B. Axelsen,Parit Bansal,Delphine Baratin,P-A Binz,M. C. Blatter,Brigitte Boeckmann,Jerven Bolleman,Emmanuel Boutet,Lionel Breuza,C Casal-Casas,E de Castro,Lorenzo Cerutti,Elisabeth Coudert,Béatrice A. Cuche,M Doche,Dolnide Dornevil,Séverine Duvaud,Anne Estreicher,L Famiglietti,M Feuermann,Elisabeth Gasteiger,Sebastien Gehant,Gerritsen,Arnaud Gos,Nadine Gruaz-Gumowski,Ursula Hinz,Chantal Hulo,J. James,Florence Jungo,Guillaume Keller,Lara,P Lemercier,J Lew,Damien Lieberherr,Thierry Lombardot,Xavier D. Martin,Patrick Masson,Anne Morgat,Teresa Batista Neto,Salvo Paesano,Ivo Pedruzzi,Sandrine Pilbout,Monica Pozzato,Manuela Pruess,Catherine Rivoire,Bernd Roechert,Maria Victoria Schneider,Christian J. A. Sigrist,K Sonesson,S Staehli,Andre Stutz,Shyamala Sundaram,Michael Tognolli,Laure Verbregue,A-L Veuthey,Cathy H. Wu,Cecilia N. Arighi,Leslie Arminski,Chuming Chen,Yongxing Chen,John S. Garavelli,Hongzhan Huang,Kati Laiho,Peter B. McGarvey,Darren A. Natale,Baris E. Suzek,C. R. Vinayaka,Qinghua Wang,Yuqi Wang,L-S Yeh,Yerramalla,Jie Zhang +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.read more
Citations
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Journal ArticleDOI
IthaGenes: an interactive database for haemoglobin variations and epidemiology.
Petros Kountouris,Carsten W. Lederer,Pavlos Fanis,Xenia Feleki,John M. Old,Marina Kleanthous +5 more
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.
Journal ArticleDOI
CPLM: a database of protein lysine modifications
Zexian Liu,Yongbo Wang,Tianshun Gao,Zhicheng Pan,Han Cheng,Qing Yang,Zhongyi Cheng,An-Yuan Guo,Jian Ren,Yu Xue +9 more
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.
Journal ArticleDOI
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'.
Journal ArticleDOI
The EcoCyc Database.
Peter D. Karp,Daniel Weaver,Suzanne M. Paley,Carol A. Fulcher,Aya Kubo,Anamika Kothari,Markus Krummenacker,Pallavi Subhraveti,Deepika Weerasinghe,Socorro Gama-Castro,Araceli M. Huerta,Luis Muñiz-Rascado,César Bonavides-Martínez,Verena Weiss,Martín Peralta-Gil,Alberto Santos-Zavaleta,Imke Schröder,Amanda Mackie,Robert P. Gunsalus,Julio Collado-Vides,Ingrid M. Keseler,Ian T. Paulsen +21 more
TL;DR: A detailed description of the data content of EcoCyc is provided and of the procedures by which this content is generated, to facilitate a system-level understanding of E. coli.
Journal ArticleDOI
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.
Ulrich Eckhard,Pitter F. Huesgen,Oliver Schilling,Caroline L. Bellac,Georgina S. Butler,Jennifer H. Cox,Antoine Dufour,Verena Goebeler,Reinhild Kappelhoff,Ulrich auf dem Keller,Theo Klein,Philipp F. Lange,Giada Marino,Charlotte J. Morrison,Anna Prudova,David Rodríguez,Amanda E. Starr,Yili Wang,Christopher M. Overall +18 more
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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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.
Journal ArticleDOI
COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.
Simon A. Forbes,Nidhi Bindal,Sally Bamford,Charlotte G. Cole,Chai Yin Kok,David Beare,Mingming Jia,Rebecca Shepherd,Kenric Leung,Andrew Menzies,Jon W. Teague,Peter J. Campbell,Michael R. Stratton,P. Andrew Futreal +13 more
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.
Journal ArticleDOI
Saccharomyces Genome Database: the genomics resource of budding yeast
J. Michael Cherry,Eurie L. Hong,Craig Amundsen,Rama Balakrishnan,Gail Binkley,Esther T. Chan,Karen R. Christie,Maria C. Costanzo,Selina S. Dwight,Stacia R. Engel,Dianna G. Fisk,Jodi E. Hirschman,Benjamin C. Hitz,Kalpana Karra,Cynthia J. Krieger,Stuart R. Miyasato,Robert S. Nash,Julie Park,Marek S. Skrzypek,Matt Simison,Shuai Weng,Edith D. Wong +21 more
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.
Journal ArticleDOI
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.
Journal ArticleDOI
InterPro in 2011: new developments in the family and domain prediction database
Sarah Hunter,Philip Jones,Alex L. Mitchell,Rolf Apweiler,Teresa K. Attwood,Alex Bateman,Thomas E. Bernard,David Binns,Peer Bork,Sarah W. Burge,Edouard de Castro,Penny Coggill,Matthew Corbett,Ujjwal Das,Louise C. Daugherty,Lauranne Duquenne,Robert D. Finn,Matthew Fraser,Julian Gough,Daniel H. Haft,Nicolas Hulo,Daniel Kahn,Elizabeth Kelly,Ivica Letunic,David M. Lonsdale,Rodrigo Lopez,Martin Madera,John Maslen,Craig McAnulla,Jennifer McDowall,Conor McMenamin,Huaiyu Mi,Prudence Mutowo-Muellenet,Nicola Mulder,Darren A. Natale,Christine A. Orengo,Sebastien Pesseat,Marco Punta,Antony F. Quinn,Catherine Rivoire,Amaia Sangrador-Vegas,Jeremy D. Selengut,Christian J. A. Sigrist,Maxim Scheremetjew,John Tate,Manjulapramila Thimmajanarthanan,Paul Thomas,Cathy H. Wu,Corin Yeats,Siew Yit Yong +49 more
TL;DR: An overview of new developments in the InterPro database and its associated software since 2009 is given, including updates to database content, curation processes and Web and programmatic interfaces.
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Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more