A continuing focus of my research is on investigating the principles (structural, energetic and dynamic) that govern the interactions of proteins, with other proteins, nucleic acids, peptides and small molecules. To that end I employ molecular simulation and modeling techniques to study these interactions at the atomic scale. I am furthermore keen on analyzing the properties of known protein structures and sequences in order to gain insight into how evolution has shaped the functional specificity of proteins.
In parallel to these molecular level investigations I am actively engaged in developing quantitative and integrative computational approaches for analyzing physical and functional interactions between proteins, protein complexes and biochemical pathways at the cellular level. My research activities closely combine the development of analysis methods and software tools, with their application to important biological problems with relevance to human health.
Shoshana Wodak is Scientific Director of the Center for Computational Biology in Toronto, Canada.Labpage Shoshana Wodak at Centre for Computational Biology
Data and Resources
iRefWeb: a resource providing a web interface to a large collection of protein–protein interactions aggregated from major specialized databases that curate protein-protein interaction data from the literature. The resource was developed in my former laboratory at the Hospital for Sick Children, Toronto Canada, but not updated since 2013: http:/wodaklab.org/iRefWeb
For a recently updated version (April 2019) of the protein-protein interaction data provided by iRefWeb please consult the iRefIndex V16 collection at: http://irefindex.vib.be/ , or at the PSCIQUIC-View: http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml
CAPRI (Critical Assessment of Predicted Interaction) website, with information on data, resources and tools relevant to modeling protein-protein interactions and complexes : www.capri-docking.org .For information on CAPRI prediction Rounds see: https://www.ebi.ac.uk/pdbe/complex-pred/capri/
- Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins. Lazar T, Guharoy M, Vranken W, Rauscher S, Wodak SJ, Tompa P. Biophys J. 2020 Jun 16;118(12):2952-2965. doi: 10.1016/j.bpj.2020.05.015. Epub 2020 May 20. PMID: 32502383
- Allostery in Its Many Disguises: From Theory to Applications. Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T. Structure. 2019 Apr 2;27(4):566-578. doi: 10.1016/j.str.2019.01.003. Epub 2019 Feb 7. PMID: 30744993
- Interplay of self-association and conformational flexibility in regulating protein function. Garton M, MacKinnon SS, Malevanets A, Wodak SJ. Philos Trans R Soc Lond B Biol Sci. 2018 Jun 19;373(1749):20170190. doi: 10.1098/rstb.2017.0190. PMID: 29735742
- Computational approaches to investigating allostery. Schueler-Furman O, Wodak SJ. Curr Opin Struct Biol. 2016 Dec;41:159-171. doi: 10.1016/j.sbi.2016.06.017. Epub 2016 Sep 6. PMID: 27607077
- Protein-protein interaction networks: the puzzling riches. Wodak SJ, Vlasblom J, Turinsky AL, Pu S. Curr Opin Struct Biol. 2013 Dec;23(6):941-53. doi: 10.1016/j.sbi.2013.08.002. Epub 2013 Sep 2. PMID: 24007795 Review.
Editorial Boards: Proteins Structure Function and BioInformatics, BMC Bioinformatics, Plos Computational Biology/Topic Pages, BioDesign Research (SPJ).
VIB-VUB Center for Structural Biology
Vrije Universiteit Brussel
Building E - Pleinlaan 2