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      Phospho.ELM: a database of phosphorylation sites—update 2011

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          Abstract

          The Phospho.ELM resource ( http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42 574 serine, threonine and tyrosine non-redundant phosphorylation sites. Several new features have been implemented, such as structural disorder/order and accessibility information and a conservation score. Additionally, the conservation of the phosphosites can now be visualized directly on the multiple sequence alignment used for the score calculation. Finally, special emphasis has been put on linking to external resources such as interaction networks and other databases.

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          The Universal Protein Resource (UniProt) in 2010

          emmanuel boutet, Claire O'Donovan, Amos Bairoch (2009)
          The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org.
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            Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.

            Liam Holt, Brian B. Tuch, Judit Villén … (2009)
            To explore the mechanisms and evolution of cell-cycle control, we analyzed the position and conservation of large numbers of phosphorylation sites for the cyclin-dependent kinase Cdk1 in the budding yeast Saccharomyces cerevisiae. We combined specific chemical inhibition of Cdk1 with quantitative mass spectrometry to identify the positions of 547 phosphorylation sites on 308 Cdk1 substrates in vivo. Comparisons of these substrates with orthologs throughout the ascomycete lineage revealed that the position of most phosphorylation sites is not conserved in evolution; instead, clusters of sites shift position in rapidly evolving disordered regions. We propose that the regulation of protein function by phosphorylation often depends on simple nonspecific mechanisms that disrupt or enhance protein-protein interactions. The gain or loss of phosphorylation sites in rapidly evolving regions could facilitate the evolution of kinase-signaling circuits.
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              SMART 6: recent updates and new developments

              Ivica Letunic, Tobias Doerks, Peer Bork (2009)
              Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains. It provides a user-friendly platform for the exploration and comparative study of domain architectures in both proteins and genes. The current release of SMART contains manually curated models for 784 protein domains. Recent developments were focused on further data integration and improving user friendliness. The underlying protein database based on completely sequenced genomes was greatly expanded and now includes 630 species, compared to 191 in the previous release. As an initial step towards integrating information on biological pathways into SMART, our domain annotations were extended with data on metabolic pathways and links to several pathways resources. The interaction network view was completely redesigned and is now available for more than 2 million proteins. In addition to the standard web access to the database, users can now query SMART using distributed annotation system (DAS) or through a simple object access protocol (SOAP) based web service.
              Article 0 comments Cited 284 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: January 2011
                Publication date (Print): January 2011
                Publication date (Electronic): 8 November 2010
                Publication date PMC-release: 8 November 2010
                Volume: 39
                Issue: Database issue , Database issue
                Pages: D261-D267
                Affiliations
                1SCB Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany, 2Genoscope (CEA - Institut de Génomique) 2, rue Gaston Cremieux. 91057 Evry, France, 3Biocomputing group, Department of Biochemical Science “A. Rossi Fanelli”, Sapienza University of Rome, P.le Aldo Moro 5, Rome, Italy, 4Victorian Centre for Functional Genomics, Peter MacCallum Cancer Center, East Melbourne, VIC 3002, Australia, 5NNF Center for Protein Research, Faculty of Health Sciences, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark and 6Biobyte solutions GmbH, 69126 Heidelberg, Germany
                Author notes
                *To whom correspondence should be addressed. Tel: +49 6221 3878451; Fax: +49 6221 387517; Email: diella@ 123456embl.de
                Correspondence may also be addressed to Toby J. Gibson. Tel: +49 6221 3878398; Fax: +49 6221 387517; Email: gibson@ 123456embl.de
                Article
                Publisher ID: gkq1104
                DOI: 10.1093/nar/gkq1104
                PMC ID: 3013696
                PubMed ID: 21062810
                SO-VID: 3d5f1f4c-74d7-42fd-85f1-a7dd3f3c1da1
                Copyright © © The Author(s) 2010. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 14 September 2010
                Date revision received : 17 October 2010
                Date accepted : 18 October 2010
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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