Tobias Doerks

Summary

Affiliation: University of Heidelberg
Country: Germany

Publications

  1. ncbi BSD: a novel domain in transcription factors and synapse-associated proteins
    Tobias Doerks
    EMBL, 69012 Heidelberg, Meyerhofstr 1, and Max Delbrueck Centrum, Berlin, Germany
    Trends Biochem Sci 27:168-70. 2002
  2. ncbi SMART 4.0: towards genomic data integration
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 32:D142-4. 2004
  3. ncbi Toward automatic reconstruction of a highly resolved tree of life
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Science 311:1283-7. 2006
  4. ncbi SMART 6: recent updates and new developments
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 37:D229-32. 2009
  5. ncbi Protein domain analysis in the era of complete genomes
    Richard R Copley
    EMBL, Meyerhofstrasse 1, Heidelberg, Germany
    FEBS Lett 513:129-34. 2002
  6. ncbi Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
    Tobias Doerks
    EMBL, 69012 Heidelberg, Meyerhofstrasse 1 and Max Delbrueck Centrum, Robert Roessle Strasse 10, D 13092 Berlin, Germany
    Nucleic Acids Res 32:6321-6. 2004
  7. ncbi Global analysis of bacterial transcription factors to predict cellular target processes
    Tobias Doerks
    EMBL, 69117 Heidelberg, Meyerhofstr 1, Germany
    Trends Genet 20:126-31. 2004
  8. ncbi SMART 7: recent updates to the protein domain annotation resource
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 40:D302-5. 2012
  9. ncbi Computational characterization of multiple Gag-like human proteins
    Monica Campillos
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Genet 22:585-9. 2006
  10. ncbi Recent improvements to the SMART domain-based sequence annotation resource
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 30:242-4. 2002

Collaborators

Detail Information

Publications16

  1. ncbi BSD: a novel domain in transcription factors and synapse-associated proteins
    Tobias Doerks
    EMBL, 69012 Heidelberg, Meyerhofstr 1, and Max Delbrueck Centrum, Berlin, Germany
    Trends Biochem Sci 27:168-70. 2002
    ..The BSD domain is characterized by three predicted alpha helices, which probably form a three-helical bundle, as well as by conserved tryptophan and phenylalanine residues, located at the C terminus of the domain...
  2. ncbi SMART 4.0: towards genomic data integration
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 32:D142-4. 2004
    ..Other improvements include the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries...
  3. ncbi Toward automatic reconstruction of a highly resolved tree of life
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Science 311:1283-7. 2006
    ..For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor...
  4. ncbi SMART 6: recent updates and new developments
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 37:D229-32. 2009
    ..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...
  5. ncbi Protein domain analysis in the era of complete genomes
    Richard R Copley
    EMBL, Meyerhofstrasse 1, Heidelberg, Germany
    FEBS Lett 513:129-34. 2002
    ....
  6. ncbi Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
    Tobias Doerks
    EMBL, 69012 Heidelberg, Meyerhofstrasse 1 and Max Delbrueck Centrum, Robert Roessle Strasse 10, D 13092 Berlin, Germany
    Nucleic Acids Res 32:6321-6. 2004
    ..However, we were able to assign pathways, cellular processes or physical complexes for 273 groups (encompassing 3624 previously functionally uncharacterized proteins)...
  7. ncbi Global analysis of bacterial transcription factors to predict cellular target processes
    Tobias Doerks
    EMBL, 69117 Heidelberg, Meyerhofstr 1, Germany
    Trends Genet 20:126-31. 2004
    ....
  8. ncbi SMART 7: recent updates to the protein domain annotation resource
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 40:D302-5. 2012
    ..An advanced full text search engine was implemented, covering the complete annotations for SMART and Pfam domains, as well as the complete set of protein descriptions, allowing users to quickly find relevant information...
  9. ncbi Computational characterization of multiple Gag-like human proteins
    Monica Campillos
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Genet 22:585-9. 2006
    ....
  10. ncbi Recent improvements to the SMART domain-based sequence annotation resource
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 30:242-4. 2002
    ..SMART output can now be easily included in users' documents. A SMART mirror has been created at http://smart.ox.ac.uk...
  11. ncbi AMOP, a protein module alternatively spliced in cancer cells
    Francesca D Ciccarelli
    Trends Biochem Sci 27:113-5. 2002
    ..The presence of AMOP in cell adhesion molecules could be indicative of a role for this domain in adhesion...
  12. ncbi DCD - a novel plant specific domain in proteins involved in development and programmed cell death
    Raimund Tenhaken
    Plant Molecular Biology, University of Frankfurt, Marie Curie Str, 9, 60439 Frankfurt, Germany
    BMC Bioinformatics 6:169. 2005
    ..We delineate the NRP-gene in soybean, which is specifically induced during this programmed cell death and contains a novel protein domain, which is commonly found in different plant proteins...
  13. ncbi CASH--a beta-helix domain widespread among carbohydrate-binding proteins
    Francesca D Ciccarelli
    Max Delbrueck Centrum, PO Box 740238, D 13092 Berlin, Germany
    Trends Biochem Sci 27:59-62. 2002
    ..The CASH domain is characterized by internal repetitions of glycines and hydrophobic residues that correspond to the repetitive units of a predicted or observed right-handed beta-helix structure of the pectate lyase superfamily...
  14. ncbi mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes
    Isabelle Behm-Ansmant
    European Molecular Biology Laboratory EMBL, Heidelberg, Germany
    Genes Dev 20:1885-98. 2006
    ..Our findings indicate that GW182 links the miRNA pathway to mRNA degradation by interacting with AGO1 and promoting decay of at least a subset of miRNA targets...
  15. ncbi STRING 7--recent developments in the integration and prediction of protein interactions
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 35:D358-62. 2007
    ..Novel features include AJAX-based web-navigation, inclusion of additional resources such as BioGRID, and detailed protein domain annotation. STRING is available at http://string.embl.de/..
  16. ncbi Systematic identification of novel protein domain families associated with nuclear functions
    Tobias Doerks
    European Molecular Biology Laboratory, 69114 Heidelberg, Germany
    Genome Res 12:47-56. 2002
    ....