Showing papers by "Toby J. Gibson published in 2007"
TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Abstract: Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
Contact: clustalw@ucd.ie
25,325 citations
TL;DR: A new BLAST search tool, complementary to retrieval by keyword and UniProt accession number, allows users to submit a protein query to search against the curated data set of phosphorylated peptides.
Abstract: Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets.
The current release of Phospho.ELM (version 7.0, July 2007) contains 4078 phospho-protein sequences covering 12 025 phospho-serine, 2362 phospho-threonine and 2083 phospho-tyrosine sites. The entries provide information about the phosphorylated proteins and the exact position of known phosphorylated instances, the kinases responsible for the modification (where known) and links to bibliographic references. The database entries have hyperlinks to easily access further information from UniProt, PubMed, SMART, ELM, MSD as well as links to the protein interaction databases MINT and STRING.
A new BLAST search tool, complementary to retrieval by keyword and UniProt accession number, allows users to submit a protein query (by sequence or UniProt accession) to search against the curated data set of phosphorylated peptides.
Phospho.ELM is available on line at: http://phospho.elm.eu.org
419 citations
Babraham Institute1, Lund University2, Los Alamos National Laboratory3, University College Dublin4, University of Provence5, University of Bordeaux6, Braunschweig University of Technology7, European Bioinformatics Institute8, University of Kassel9, German Cancer Research Center10, University of Tübingen11, Max Planck Society12, Uppsala University13, Leiden University Medical Center14, Wellcome Trust Sanger Institute15, VU University Amsterdam16, Royal Institute of Technology17, University of Zurich18, University of Rijeka19, University of Konstanz20, Technische Universität München21
TL;DR: ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human proteome.
Abstract: ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human proteome. Given the huge diversity of the proteome, the scale of the project is potentially immense but nevertheless feasible in the context of a pan-European or even worldwide coordination.
238 citations
TL;DR: In the version of the article originally published, Manfred Koegl's name was misspelled and Zoltan Konthur's affiliation was incorrect; it should be Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
Abstract: Nat. Methods 4, 13–17 (2007); published online 28 December 2006; corrected after print 18 January 2007. In the version of the article originally published, Manfred Koegl's name was misspelled. Additionally, Zoltan Konthur's affiliation was incorrect; it should be Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
2 citations