Affiliation: Center for Biological Sequence Analysis
- PhosphoBase: a database of phosphorylation sitesN Blom
Center for Biological Sequence Analysis, Department of Chemistry, Building 207, The Technical University of Denmark, DK 2800 Lyngby, Denmark
Nucleic Acids Res 26:382-6. 1998..PhosphoBase is available on the WWW at http://www.cbs.dtu.dk/databases/PhosphoBase/..
- Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequenceNikolaj Blom
Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby, Denmark
Proteomics 4:1633-49. 2004..The new server, NetPhosK, is made publicly available at the URL http://www.cbs.dtu.dk/services/NetPhosK/. The issues of underestimation, over-prediction and strategies for improving prediction specificity are also discussed...
- Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteinsFrancesca Diella
Cellzome AG, Heidelberg, Germany
BMC Bioinformatics 5:79. 2004..The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins...
- Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathologyLars Kiemer
Center for Biological Sequence Analysis BioCentrum DTU, Technical University of Denmark DK 2800 Lyngby
BMC Bioinformatics 5:72. 2004..Prompted by this, we set out to analyse and predict cleavage by the coronavirus main proteinase using computational methods...
- Linear motif atlas for phosphorylation-dependent signalingMartin Lee Miller
Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
Sci Signal 1:ra2. 2008..The atlas is available as a community resource (http://netphorest.info)...
- Kinase-specific prediction of protein phosphorylation sitesMartin L Miller
Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
Methods Mol Biol 527:299-310, x. 2009..Finally, we point to possible developments with the intention of providing the community with improved and additional phosphorylation predictors for large-scale modeling of cellular signaling networks...
- NetPhosBac - a predictor for Ser/Thr phosphorylation sites in bacterial proteinsMartin Lee Miller
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
Proteomics 9:116-25. 2009..In conclusion, NetPhosBac clearly illustrates the advantage of taxa-specific predictors and we hope it will provide a useful asset to the microbiological community...
- Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2Martin Lee Miller
Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, DK 2800 Lyngby, Denmark
Mol Cell Proteomics 7:181-92. 2008..Our decomposition of the in vivo Tyr(P) proteome furthermore suggests that two-thirds of the Tyr(P) sites mediate interaction, whereas the remaining third govern processes such as enzyme activation and nucleic acid binding...
- NetAcet: prediction of N-terminal acetylation sitesLars Kiemer
Center for Biological Sequence Analysis, BioCentrum-DTU Building 208 Technical University of Denmark, DK-2800 Lyngby, Denmark
Bioinformatics 21:1269-70. 2005..We obtain correlation coefficients close to 0.7 on yeast data and a sensitivity up to 74% on mammalian data, suggesting that the method is valid for eukaryotic NatA orthologs...
- Feature-based prediction of non-classical and leaderless protein secretionJannick Dyrløv Bendtsen
Center for Biological Sequence Analysis BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
Protein Eng Des Sel 17:349-56. 2004..By scanning the entire human proteome we identified new proteins potentially undergoing non-classical secretion. Predictions can be made at http://www.cbs.dtu.dk/services/SecretomeP...