Research Topics
| T DoerksSummaryAffiliation: European Molecular Biology Laboratory Country: Germany Publications
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Detail Information
Publications
DDT -- a novel domain in different transcription and chromosome remodeling factorsT Doerks
European Molecular Biology Laboratory, 69012 Heidelberg, Germany
Trends Biochem Sci 26:145-6. 2001..This domain is characterized by a number of conserved aromatic and charged residues and is predicted to consist of three alpha helices. Recent studies indicate a likely DNA-binding function for the DDT domain...
Systematic identification of novel protein domain families associated with nuclear functionsTobias Doerks
European Molecular Biology Laboratory, 69114 Heidelberg, Germany
Genome Res 12:47-56. 2002....- eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotationsJ Muller
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nucleic Acids Res 38:D190-5. 2010..Users can access the complete set of orthologous groups via a web interface at: http://eggnog.embl.de... - Quantitative assessment of protein function prediction from metagenomics shotgun sequencesE D Harrington
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Proc Natl Acad Sci U S A 104:13913-8. 2007..Our results further suggest that, although functions can be inferred for most proteins on earth, many functions remain to be discovered in numerous small, rare protein families... - Quantitative phylogenetic assessment of microbial communities in diverse environmentsC von Mering
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Science 315:1126-30. 2007..The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time... - CASH--a beta-helix domain widespread among carbohydrate-binding proteinsFrancesca 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... - DCD - a novel plant specific domain in proteins involved in development and programmed cell deathRaimund 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... - eggNOG: automated construction and annotation of orthologous groups of genesLars Juhl Jensen
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nucleic Acids Res 36:D250-4. 2008..Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl.de... - STRING 7--recent developments in the integration and prediction of protein interactionsChristian 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/.. - Toward automatic reconstruction of a highly resolved tree of lifeFrancesca 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... - Recent improvements to the SMART domain-based sequence annotation resourceIvica 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... - SMART 4.0: towards genomic data integrationIvica 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... - BSD: a novel domain in transcription factors and synapse-associated proteinsTobias 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... - Protein domain analysis in the era of complete genomesRichard R Copley
EMBL, Meyerhofstrasse 1, Heidelberg, Germany
FEBS Lett 513:129-34. 2002.... - Global analysis of bacterial transcription factors to predict cellular target processesTobias Doerks
EMBL, 69117 Heidelberg, Meyerhofstr 1, Germany
Trends Genet 20:126-31. 2004....