Sun, 27 Jul 2008 08:18:33 BST CiteULike: jyuh's Stümpflen http://www.citeulike.org/user/jyuh/author/Stümpflen CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/jyuh/article/2782605 <i>Nucleic acids research, Vol. 36, No. Database issue. (January 2008)</i><br /><br />The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse. To cope with the task of global in-depth genome annotation has become unfeasible. Therefore, our efforts are dedicated to three levels of annotation: (i) the curation of selected genomes, in particular from fungal and plant taxa (e.g. CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de). MIPS: analysis and annotation of genome information in 2007. HW Mewes S Dietmann D Frishman R Gregory G Mannhaupt KF Mayer M Münsterkötter A Ruepp M Spannagl V Stümpflen T Rattei Nucleic acids research, Vol. 36, No. Database issue. (January 2008) 2008-05-10T08:57:38-00:00 2008 Nucleic acids research 1362-4962 36 Database issue no-tag http://www.citeulike.org/user/jyuh/article/2249143 <i>Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)</i><br /><br />Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scientific literature from expert annotators. Information about protein complexes includes protein complex names, subunits, literature references as well as the function of the complexes. For functional annotation, we use the FunCat catalogue that enables to organize the protein complex space into biologically meaningful subsets. The database contains more than 1750 protein complexes that are built from 2400 different genes, thus representing 12% of the protein-coding genes in human. A web-based system is available to query, view and download the data. CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases. Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes. CORUM: the comprehensive resource of mammalian protein complexes. A Ruepp B Brauner I Dunger-Kaltenbach G Frishman C Montrone M Stransky B Waegele T Schmidt ON Doudieu V Stümpflen HW Mewes Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008) 2008-01-18T03:50:41-00:00 2008 Nucleic Acids Res 1362-4962 36 Database issue no-tag http://www.citeulike.org/user/jyuh/article/1544639 <i>Nature Biotechnology, Vol. 25, No. 8. (08 August 2007), pp. 894-898.</i> The minimum information required for reporting a molecular interaction experiment (MIMIx) Sandra Orchard Lukasz Salwinski Samuel Kerrien Luisa Montecchi-Palazzi Matthias Oesterheld Volker Stümpflen Arnaud Ceol Andrew Chatr-Aryamontri John Armstrong Peter Woollard John Salama Susan Moore Jérôme Wojcik Gary Bader Marc Vidal Michael Cusick Mark Gerstein Anne-Claude Gavin Giulio Superti-Furga Jack Greenblatt Joel Bader Peter Uetz Mike Tyers Pierre Legrain Stan Fields Nicola Mulder Michael Gilson Michael Niepmann Lyle Burgoon Javier Carlos Prieto Victoria Perreau Chris Hogue Hans-Werner Mewes Rolf Apweiler Ioannis Xenarios David Eisenberg Gianni Cesareni Henning Hermjakob doi:10.1038/nbt1324 Nature Biotechnology, Vol. 25, No. 8. (08 August 2007), pp. 894-898. 2007-08-09T00:39:24-00:00 2007 Nature Biotechnology 1087-0156 25 8 894 898 Nature Publishing Group no-tag