Publications

Found 145 results
Filters: Author is Shoshana J Wodak  [Clear All Filters]
2016
Bohnuud, T., Luo L., Wodak S. J., Bonvin A. M. J. J., Weng Z., Vajda S., Schueler-Furman O., and Kozakov D., "A benchmark testing ground for integrating homology modeling and protein docking.", Proteins, 2016 May 12.
Schueler-Furman, O., and Wodak S. J., "Computational approaches to investigating allostery.", Curr Opin Struct Biol, vol. 41, pp. 159-171, 2016 Sep 05.
Shukla, A. K., and Wodak S. J., "Editorial overview: Multi-protein assemblies in signaling.", Curr Opin Struct Biol, 2016 Nov 23.
Lensink, M. F., Velankar S., and Wodak S. J., "Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition.", Proteins, 2016 Nov 16.
Lensink, M. F., Velankar S., Kryshtafovych A., Huang S-Y., Schneidman-Duhovny D., Sali A., Segura J., Fernandez-Fuentes N., Viswanath S., Elber R., et al., "Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.", Proteins, vol. 84 Suppl 1, pp. 323-48, 2016 Sep.
2015
Marcon, E., Jain H., Bhattacharya A., Guo H., Phanse S., Pu S., Byram G., Collins B. C., Dowdell E., Fenner M., et al., "Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation.", Nat Methods, vol. 12, issue 8, pp. 725-31, 2015 Aug.
Pu, S., Vlasblom J., Turinsky A., Marcon E., Phanse S., Trimble S. Smiley, Olsen J., Greenblatt J., Emili A., and Wodak S. J., "Extracting high confidence protein interactions from affinity purification data: at the crossroads.", J Proteomics, vol. 118, pp. 63-80, 2015 Apr 06.
Wodak, S. J., Malevanets A., and Mackinnon S. S., "The Landscape of Intertwined Associations in Homooligomeric Proteins.", Biophys J, vol. 109, issue 6, pp. 1087-100, 2015 Sep 15.
Mackinnon, S. S., and Wodak S. J., "Landscape of intertwined associations in multi-domain homo-oligomeric proteins.", J Mol Biol, vol. 427, issue 2, pp. 350-70, 2015 Jan 30.
2014
Lensink, M. F., Moal I. H., Bates P. A., Kastritis P. L., Melquiond A. S. J., Karaca E., Schmitz C., van Dijk M., Bonvin A. M. J. J., Eisenstein M., et al., "Blind prediction of interfacial water positions in CAPRI.", Proteins, vol. 82, issue 4, pp. 620-32, 2014 Apr.
Marcon, E., Ni Z., Pu S., Turinsky A. L., Trimble S. Smiley, Olsen J. B., Silverman-Gavrila R., Silverman-Gavrila L., Phanse S., Guo H., et al., "Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation.", Cell Rep, vol. 8, issue 1, pp. 297-310, 2014 Jul 10.
Qiao, W., Wang W., Laurenti E., Turinsky A. L., Wodak S. J., Bader G. D., Dick J. E., and Zandstra P. W., "Intercellular network structure and regulatory motifs in the human hematopoietic system.", Mol Syst Biol, vol. 10, pp. 741, 2014 Jul 15.
Turinsky, A. L., Razick S., Turner B., Donaldson I. M., and Wodak S. J., "Navigating the global protein-protein interaction landscape using iRefWeb.", Methods Mol Biol, vol. 1091, pp. 315-31, 2014.
Lensink, M. F., and Wodak S. J., "Score_set: a CAPRI benchmark for scoring protein complexes.", Proteins, vol. 82, issue 11, pp. 3163-9, 2014 Nov.
2013
Moretti, R., Fleishman S. J., Agius R., Torchala M., Bates P. A., Kastritis P. L., Rodrigues J. P. G. L. M., Trellet M., Bonvin A. M. J. J., Cui M., et al., "Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.", Proteins, vol. 81, issue 11, pp. 1980-7, 2013 Nov.
Lensink, M. F., and Wodak S. J., "Docking, scoring, and affinity prediction in CAPRI.", Proteins, vol. 81, issue 12, pp. 2082-95, 2013 Dec.
Mackinnon, S. S., Malevanets A., and Wodak S. J., "Intertwined associations in structures of homooligomeric proteins.", Structure, vol. 21, issue 4, pp. 638-49, 2013 Apr 2.
Jiang, J-X., Aitken K. J., Sotiropoulos C., Sotiropolous C., Kirwan T., Panchal T., Zhang N., Pu S., Wodak S. J., Tolg C., et al., "Phenotypic switching induced by damaged matrix is associated with DNA methyltransferase 3A (DNMT3A) activity and nuclear localization in smooth muscle cells (SMC).", PLoS One, vol. 8, issue 8, pp. e69089, 2013.
Wodak, S. J., Vlasblom J., Turinsky A. L., and Pu S., "Protein-protein interaction networks: the puzzling riches.", Curr Opin Struct Biol, vol. 23, issue 6, pp. 941-53, 2013 Dec.
2012
Havugimana, P. C., G Hart T., Nepusz T., Yang H., Turinsky A. L., Li Z., Wang P. I., Boutz D. R., Fong V., Phanse S., et al., "A census of human soluble protein complexes.", Cell, vol. 150, issue 5, pp. 1068-81, 2012 Aug 31.
Babu, M., Vlasblom J., Pu S., Guo X., Graham C., Bean B. D. M., Burston H. E., Vizeacoumar F. J., Snider J., Phanse S., et al., "Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.", Nature, vol. 489, issue 7417, pp. 585-9, 2012 Sep 27.
Wodak, S. J., "Next-generation protein engineering targets influenza.", Nat Biotechnol, vol. 30, issue 6, pp. 502-4, 2012 Jun.
Fiume, M., Smith E. J. M., Brook A., Strbenac D., Turner B., Mezlini A. M., Robinson M. D., Wodak S. J., and Brudno M., "Savant Genome Browser 2: visualization and analysis for population-scale genomics.", Nucleic Acids Res, vol. 40, issue Web Server issue, pp. W615-21, 2012 Jul.
Wodak, S. J., Mietchen D., Collings A. M., Russell R. B., and Bourne P. E., "Topic pages: PLoS Computational Biology meets Wikipedia.", PLoS Comput Biol, vol. 8, issue 3, pp. e1002446, 2012.
2011
Leung, E., Datti A., Cossette M., Goodreid J., McCaw S. E., Mah M., Nakhamchik A., Ogata K., Bakkouri M. El, Cheng Y-Q., et al., "Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease.", Chem Biol, vol. 18, issue 9, pp. 1167-78, 2011 Sep 23.

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