Center for Computational and Theoretical Biology

Protein Evolution

Summary

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.  

Publications

2016[ to top ]
  • {{W}{H}{A}{M}{Y} is a novel actin polymerase promoting myoblast fusion, macrophage cell motility and sensory organ development in {D}rosophila}. Brinkmann, K.; Winterhoff, M.; Onel, S. F.; Schultz, J.; Faix, J.; Bogdan, S. In J. Cell. Sci., 129(3), bll 604–620. 2016.
  • {{A}{L}{V}{I}{S}: 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., 44(8), bl e77. 2016.
  • {{G}ating of the two-pore cation channel {A}t{T}{P}{C}1 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), 18(5), bll 750–760. 2016.
2015[ to top ]
  • {{I}dentification of divergent {W}{H}2 motifs by {H}{M}{M}-{H}{M}{M} alignments}. Weiss, C.; Schultz, J. In BMC Res Notes, 8(1), bl 18. 2015.
2014[ to top ]
  • {{F}{H}{O}{D} proteins in actin dynamics-a formin’ class of its own}. Bechtold, M.; Schultz, J.; Bogdan, S. In Small GTPases, 5(2), bll 1–6. 2014.
  • {{E}volutionary and {S}tructural {A}nalyses of the {M}ammalian {H}aloacid {D}ehalogenase-{T}ype {P}hosphatases {A}{U}{M} and {C}hronophin {P}rovide {I}nsight into the {B}asis of their {D}ifferent {S}ubstrate {S}pecificities}. Seifried, A.; Knobloch, G.; Duraphe, P. S.; Segerer, G.; Manhard, J.; Schindelin, H.; Schultz, J.; Gohla, A. In J. Biol. Chem., 289(6), bll 3416–31. 2014.
2013[ to top ]
  • {{H}uman {H}{A}{D} phosphatases: structure, mechanism, and roles in health and disease}. Seifried, A.; Schultz, J.; Gohla, A. In FEBS J., 280(2), bll 549–571. 2013.
  • Formin’ cellular structures. Bogdan, Sven; Schultz, Jörg; Grosshans, Jörg. In Communicative & Integrative Biology, 6(6), bl e27634. 2013.
  • {{T}he bilaterian roots of cordon-bleu}. Schultz, J.; Terhoeven, N. In BMC Res Notes, 6(1), bl 393. 2013.
2010[ to top ]
  • {{P}rotein interaction networks--more than mere modules}. Pinkert, S.; Schultz, J.; Reichardt, J. In PLoS Comput. Biol., 6, bl e1000659. 2010.
  • {{E}volutionary 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, 5, bl e15788. 2010.
2009[ to top ]
  • {{P}ositive selection in tick saliva proteins of the {S}alp15 family}. Schwalie, P. C.; Schultz, J. In J. Mol. Evol., 68, bll 186–191. 2009.
  • {{P}artially-supervised protein subclass discovery with simultaneous annotation of functional residues}. Georgi, B.; Schultz, J.; Schliep, A. In BMC Struct. Biol., 9, bl 68. 2009.
  • {{E}volutionary flexibility of protein complexes}. Seidl, M. F.; Schultz, J. In BMC Evol. Biol., 9, bl 155. 2009.
  • {{D}etecting 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., 37, bll 5959–5968. 2009.
  • {{A} kinome of 2600 in the ciliate {P}aramecium tetraurelia}. Bemm, F.; Schwarz, R.; Forster, F.; Schultz, J. In FEBS Lett., 583, bll 3589–3592. 2009.
2008[ to top ]
  • {{E}volution of an {R}{N}{P} assembly system: a minimal {S}{M}{N} complex facilitates formation of {U}sn{R}{N}{P}s in {D}rosophila melanogaster}. Kroiss, M.; Schultz, J.; Wiesner, J.; Chari, A.; Sickmann, A.; Fischer, U. In Proc. Natl. Acad. Sci. U.S.A., 105, bll 10045–10050. 2008.
2006[ to top ]
  • {{M}odelling interaction sites in protein domains with interaction profile hidden {M}arkov models}. Friedrich, T.; Pils, B.; Dandekar, T.; Schultz, J.; Muller, T. In Bioinformatics, 22, bll 2851–2857. 2006.
2005[ to top ]
  • {{V}ariation in structural location and amino acid conservation of functional sites in protein domain families}. Pils, B.; Copley, R. R.; Schultz, J. In BMC Bioinformatics, 6, bl 210. 2005.