Johannes Söding

Summary

Affiliation: Max Planck Institute for Biological Cybernetics
Country: Germany

Publications

  1. pmc HHsenser: exhaustive transitive profile search using HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 34:W374-8. 2006
  2. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
    Bioinformatics 21:951-60. 2005
  3. pmc HHrep: de novo protein repeat detection and the origin of TIM barrels
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 34:W137-42. 2006
  4. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
  5. pmc A galaxy of folds
    Vikram Alva
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen 72076, Germany
    Protein Sci 19:124-30. 2010
  6. pmc The MPI Bioinformatics Toolkit for protein sequence analysis
    Andreas Biegert
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 34:W335-9. 2006
  7. pmc TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences
    Manjunatha R Karpenahalli
    Department of Protein Evolution, Max Planck lnstitute for Developmental Biology, Spemannstrasse 35, D 72076 Tubingen, Germany
    BMC Bioinformatics 8:2. 2007
  8. pmc REPPER--repeats and their periodicities in fibrous proteins
    Markus Gruber
    Max Planck Institute for Developmental Biology Spemannstr 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W239-43. 2005
  9. pmc HHomp--prediction and classification of outer membrane proteins
    Michael Remmert
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 37:W446-51. 2009
  10. ncbi More than the sum of their parts: on the evolution of proteins from peptides
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen, Germany
    Bioessays 25:837-46. 2003

Collaborators

Detail Information

Publications16

  1. pmc HHsenser: exhaustive transitive profile search using HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 34:W374-8. 2006
    ..HHsenser can be accessed at http://hhsenser.tuebingen.mpg.de/. It has also been integrated into our structure and function prediction server HHpred (http://hhpred.tuebingen.mpg.de/) to improve predictions for near-singleton sequences...
  2. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
    Bioinformatics 21:951-60. 2005
    ..Speed: HHsearch scans a query of 200 residues against 3691 domains in 33 s on an AMD64 2GHz PC. This is 10 times faster than PROF_SIM and 17 times faster than COMPASS...
  3. pmc HHrep: de novo protein repeat detection and the origin of TIM barrels
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 34:W137-42. 2006
    ..This symmetry might be the trace of an ancient origin through duplication of a betaalphabetaalpha or betaalpha unit. HHrep can be accessed at http://hhrep.tuebingen.mpg.de...
  4. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
    ..A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at http://protevo.eb.tuebingen.mpg.de/hhpred...
  5. pmc A galaxy of folds
    Vikram Alva
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen 72076, Germany
    Protein Sci 19:124-30. 2010
    ..Our galaxy of folds summarizes, in a single image, most known and many yet undescribed homologous relationships between protein superfamilies, providing new insights into the evolution of protein domains...
  6. pmc The MPI Bioinformatics Toolkit for protein sequence analysis
    Andreas Biegert
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 34:W335-9. 2006
    ..The Toolkit framework and the tools developed in-house will be packaged and freely available under the GNU Lesser General Public Licence (LGPL). The Toolkit can be accessed at http://toolkit.tuebingen.mpg.de...
  7. pmc TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences
    Manjunatha R Karpenahalli
    Department of Protein Evolution, Max Planck lnstitute for Developmental Biology, Spemannstrasse 35, D 72076 Tubingen, Germany
    BMC Bioinformatics 8:2. 2007
    ..Several resources are available for the prediction of TPRs, however, they often fail to detect divergent repeat units...
  8. pmc REPPER--repeats and their periodicities in fibrous proteins
    Markus Gruber
    Max Planck Institute for Developmental Biology Spemannstr 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W239-43. 2005
    ..REPPER is available at http://protevo.eb.tuebingen.mpg.de/repper...
  9. pmc HHomp--prediction and classification of outer membrane proteins
    Michael Remmert
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 37:W446-51. 2009
    ..In Escherichia coli, HHomp identifies 57 out of 59 known OMPs and correctly assigns them to their functional subgroups. HHomp can be accessed at http://toolkit.tuebingen.mpg.de/hhomp...
  10. ncbi More than the sum of their parts: on the evolution of proteins from peptides
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen, Germany
    Bioessays 25:837-46. 2003
    ..Their association into larger structures and eventual fusion into polypeptide chains would have allowed them to become independent of their RNA scaffold, leading to the evolution of a novel type of macromolecule: the folded protein...
  11. pmc On the origin of the histone fold
    Vikram Alva
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen, Germany
    BMC Struct Biol 7:17. 2007
    ..We have searched for the evolutionary origin of this fold using sequence and structure comparisons, based on the hypothesis that folded proteins evolved by combination of an ancestral set of peptides, the antecedent domain segments...
  12. ncbi Evolution of the beta-propeller fold
    Indronil Chaudhuri
    Department for Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
    Proteins 71:795-803. 2008
    ..The observation of propellers with nearly identical blades in genomic sequences show that these mechanisms are still operating today...
  13. ncbi ScbA from Streptomyces coelicolor A3(2) has homology to fatty acid synthases and is able to synthesize gamma-butyrolactones
    Nai Hua Hsiao
    Mikrobiologie Biotechnologie, Eberhard Karls Universitat Tubingen, Auf der Morgenstelle 28, 72076 Tubingen, Germany
    Microbiology 153:1394-404. 2007
    ....
  14. ncbi AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels
    Murray Coles
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 13:919-28. 2005
    ....
  15. ncbi Retroactive, a membrane-anchored extracellular protein related to vertebrate snake neurotoxin-like proteins, is required for cuticle organization in the larva of Drosophila melanogaster
    Bernard Moussian
    Department of Genetics, Max Planck Institute for Developmental Biology, Tubingen, Germany
    Dev Dyn 233:1056-63. 2005
    ..We propose that this binding function of Rtv may assist the organization of chitin fibers at the epidermal cell surface during cuticle assembly...
  16. ncbi Comparative analysis of coiled-coil prediction methods
    Markus Gruber
    Max Planck Institute for Developmental Biology, Spemannstr 35, 72076 Tubingen, Germany
    J Struct Biol 155:140-5. 2006
    ....