Center for Computational and Theoretical Biology

Protein Evolution


The protein universe covers an enormous functional diversity although occupying only a tiny fraction of sequence space. Frequently in collaboration with experimental groups, we use methods like homology detection, domain annotation, phylogeny reconstruction, structure prediction and evolutionary rate analyses to pinpoint sequence changes correlated with functional innovations.  


[ 2016 ] [ 2015 ] [ 2014 ] [ 2013 ] [ 2010 ] [ 2009 ] [ 2008 ] [ 2006 ] [ 2005 ]

2016 [ nach oben ]

  • WHAMY is a novel actin polymerase promoting myoblast fusion, macrophage cell motility and sensory organ development in Drosophila. Brinkmann, K.; Winterhoff, M.; Onel, S. F.; Schultz, J.; Faix, J.; Bogdan, S. in J. Cell. Sci. (2016). 129(3) 604–620.
  • Gating of the two-pore cation channel AtTPC1 in the plant vacuole is based on a single voltage-sensing domain. Ja?lan, D.; Mueller, T. D.; Becker, D.; Schultz, J.; Cuin, T. A.; Marten, I.; Dreyer, I.; Schonknecht, G.; Hedrich, R. in Plant Biol (Stuttg) (2016). 18(5) 750–760.
  • ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments. Schwarz, R. F.; Tamuri, A. U.; Kultys, M.; King, J.; Godwin, J.; Florescu, A. M.; Schultz, J.; Goldman, N. in Nucleic Acids Res. (2016). 44(8) e77.

2015 [ nach oben ]

  • Identification of divergent WH2 motifs by HMM-HMM alignments. Weiss, C.; Schultz, J. in BMC Res Notes (2015). 8(1) 18.

2014 [ nach oben ]

  • FHOD proteins in actin dynamics-a formin’ class of its own. Bechtold, M.; Schultz, J.; Bogdan, S. in Small GTPases (2014). 5(2) 1–6.
  • Evolutionary and Structural Analyses of the Mammalian Haloacid Dehalogenase-Type Phosphatases AUM and Chronophin Provide Insight into the Basis of their Different Substrate Specificities. Seifried, A.; Knobloch, G.; Duraphe, P. S.; Segerer, G.; Manhard, J.; Schindelin, H.; Schultz, J.; Gohla, A. in J. Biol. Chem. (2014). 289(6) 3416–31.

2013 [ nach oben ]

  • The bilaterian roots of cordon-bleu. Schultz, J.; Terhoeven, N. in BMC Res Notes (2013). 6(1) 393.
  • Human HAD phosphatases: structure, mechanism, and roles in health and disease. Seifried, A.; Schultz, J.; Gohla, A. in FEBS J. (2013). 280(2) 549–571.
  • Formin’ cellular structures. Bogdan, Sven; Schultz, Jörg; Grosshans, Jörg in Communicative & Integrative Biology (2013). 6(6) e27634.

2010 [ nach oben ]

  • Protein interaction networks--more than mere modules. Pinkert, S.; Schultz, J.; Reichardt, J. in PLoS Comput. Biol. (2010). 6 e1000659.
  • Evolutionary distances in the twilight zone--a rational kernel approach. Schwarz, R. F.; Fletcher, W.; Forster, F.; Merget, B.; Wolf, M.; Schultz, J.; Markowetz, F. in PLoS ONE (2010). 5 e15788.

2009 [ nach oben ]

  • Positive selection in tick saliva proteins of the Salp15 family. Schwalie, P. C.; Schultz, J. in J. Mol. Evol. (2009). 68 186–191.
  • Partially-supervised protein subclass discovery with simultaneous annotation of functional residues. Georgi, B.; Schultz, J.; Schliep, A. in BMC Struct. Biol. (2009). 9 68.
  • Evolutionary flexibility of protein complexes. Seidl, M. F.; Schultz, J. in BMC Evol. Biol. (2009). 9 155.
  • Detecting species-site dependencies in large multiple sequence alignments. Schwarz, R.; Seibel, P. N.; Rahmann, S.; Schoen, C.; Huenerberg, M.; Muller-Reible, C.; Dandekar, T.; Karchin, R.; Schultz, J.; Muller, T. in Nucleic Acids Res. (2009). 37 5959–5968.
  • A kinome of 2600 in the ciliate Paramecium tetraurelia. Bemm, F.; Schwarz, R.; Forster, F.; Schultz, J. in FEBS Lett. (2009). 583 3589–3592.

2008 [ nach oben ]

  • Evolution of an RNP assembly system: a minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster. Kroiss, M.; Schultz, J.; Wiesner, J.; Chari, A.; Sickmann, A.; Fischer, U. in Proc. Natl. Acad. Sci. U.S.A. (2008). 105 10045–10050.

2006 [ nach oben ]

  • Modelling interaction sites in protein domains with interaction profile hidden Markov models. Friedrich, T.; Pils, B.; Dandekar, T.; Schultz, J.; Muller, T. in Bioinformatics (2006). 22 2851–2857.

2005 [ nach oben ]

  • Variation in structural location and amino acid conservation of functional sites in protein domain families. Pils, B.; Copley, R. R.; Schultz, J. in BMC Bioinformatics (2005). 6 210.