Shoshana J Wodak - Publications

1974 VIB-VUB Brussels Belgium 
Molecular simulations, biophysics, bioinformatics, protei-protein interaction, proteomics

69 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Wodak SJ, Janin J. Modeling protein assemblies: CAPRI 15 years hence 6(th) CAPRI evaluation meeting April 17-19 Tel-Aviv Israel. Proteins. PMID 28019680 DOI: 10.1002/prot.25233  1
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Wodak SJ, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/prot.25007  0.52
2015 Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, ... ... Wodak SJ, et al. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nature Methods. PMID 26121405 DOI: 10.1038/nmeth.3472  1
2015 Pu S, Vlasblom J, Turinsky A, Marcon E, Phanse S, Trimble SS, Olsen J, Greenblatt J, Emili A, Wodak SJ. Extracting high confidence protein interactions from affinity purification data: at the crossroads. Journal of Proteomics. 118: 63-80. PMID 25782749 DOI: 10.1016/j.jprot.2015.03.009  1
2014 Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, Bader GD, Dick JE, Zandstra PW. Intercellular network structure and regulatory motifs in the human hematopoietic system. Molecular Systems Biology. 10: 741. PMID 25028490 DOI: 10.15252/msb.20145141  1
2014 Marcon E, Ni Z, Pu S, Turinsky AL, Trimble SS, Olsen JB, Silverman-Gavrila R, Silverman-Gavrila L, Phanse S, Guo H, Zhong G, Guo X, Young P, Bailey S, Roudeva D, ... ... Wodak SJ, et al. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Cell Reports. 8: 297-310. PMID 24981860 DOI: 10.1016/j.celrep.2014.05.050  1
2014 Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. Navigating the global protein-protein interaction landscape using iRefWeb. Methods in Molecular Biology (Clifton, N.J.). 1091: 315-31. PMID 24203342 DOI: 10.1007/978-1-62703-691-7_22  1
2014 Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, ... ... Wodak SJ, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/prot.24439  1
2014 Emili A, Wodak S, Greenblatt J. Systems analysis of chromatin-related protein complexes in cancer Systems Analysis of Chromatin-Related Protein Complexes in Cancer. 2147483647: 1-316. DOI: 10.1007/978-1-4614-7931-4  1
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Wodak SJ, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/prot.24356  1
2013 Grafodatskaya D, Chung BH, Butcher DT, Turinsky AL, Goodman SJ, Choufani S, Chen YA, Lou Y, Zhao C, Rajendram R, Abidi FE, Skinner C, Stavropoulos J, Bondy CA, Hamilton J, ... Wodak S, et al. Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C. Bmc Medical Genomics. 6: 1. PMID 23356856 DOI: 10.1186/1755-8794-6-1  1
2012 Babu M, Vlasblom J, Pu S, Guo X, Graham C, Bean BD, Burston HE, Vizeacoumar FJ, Snider J, Phanse S, Fong V, Tam YY, Davey M, Hnatshak O, Bajaj N, ... ... Wodak SJ, et al. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature. 489: 585-9. PMID 22940862 DOI: 10.1038/nature11354  1
2012 Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, ... ... Wodak SJ, et al. A census of human soluble protein complexes. Cell. 150: 1068-81. PMID 22939629 DOI: 10.1016/j.cell.2012.08.011  1
2012 Fiume M, Smith EJ, Brook A, Strbenac D, Turner B, Mezlini AM, Robinson MD, Wodak SJ, Brudno M. Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Research. 40: W615-21. PMID 22638571 DOI: 10.1093/nar/gks427  1
2012 Wodak SJ, Mietchen D, Collings AM, Russell RB, Bourne PE. Topic pages: PLoS Computational Biology meets Wikipedia. Plos Computational Biology. 8: e1002446. PMID 22479174 DOI: 10.1371/journal.pcbi.1002446  1
2011 Babu M, Díaz-Mejía JJ, Vlasblom J, Gagarinova A, Phanse S, Graham C, Yousif F, Ding H, Xiong X, Nazarians-Armavil A, Alamgir M, Ali M, Pogoutse O, Pe'er A, Arnold R, ... ... Wodak SJ, et al. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. Plos Genetics. 7: e1002377. PMID 22125496 DOI: 10.1371/journal.pgen.1002377  1
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Wodak SJ, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/j.jmb.2011.09.031  1
2011 Leung E, Datti A, Cossette M, Goodreid J, McCaw SE, Mah M, Nakhamchik A, Ogata K, El Bakkouri M, Cheng YQ, Wodak SJ, Eger BT, Pai EF, Liu J, Gray-Owen S, et al. Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease. Chemistry & Biology. 18: 1167-78. PMID 21944755 DOI: 10.1016/j.chembiol.2011.07.023  1
2011 Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. Interaction databases on the same page. Nature Biotechnology. 29: 391-3. PMID 21552234 DOI: 10.1038/nbt.1867  1
2011 Hao Y, Merkoulovitch A, Vlasblom J, Pu S, Turinsky AL, Roudeva D, Turner B, Greenblatt J, Wodak SJ. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics (Oxford, England). 27: 883-4. PMID 21257609 DOI: 10.1093/bioinformatics/btr035  1
2011 Turinsky AL, Turner B, Borja RC, Gleeson JA, Heath M, Pu S, Switzer T, Dong D, Gong Y, On T, Xiong X, Emili A, Greenblatt J, Parkinson J, Zhang Z, ... Wodak SJ, et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Research. 39: D889-94. PMID 20876685 DOI: 10.1093/nar/gkq857  1
2010 Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. Literature curation of protein interactions: measuring agreement across major public databases. Database : the Journal of Biological Databases and Curation. 2010: baq026. PMID 21183497 DOI: 10.1093/database/baq026  1
2010 Pu S, Turinsky AL, Vlasblom J, On T, Xiong X, Emili A, Zhang Z, Greenblatt J, Parkinson J, Wodak SJ. Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human. Plos One. 5: e14122. PMID 21124763 DOI: 10.1371/journal.pone.0014122  1
2010 Turner B, Razick S, Turinsky AL, Vlasblom J, Crowdy EK, Cho E, Morrison K, Donaldson IM, Wodak SJ. iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database : the Journal of Biological Databases and Curation. 2010: baq023. PMID 20940177 DOI: 10.1093/database/baq023  1
2010 Santos MA, Turinsky AL, Ong S, Tsai J, Berger MF, Badis G, Talukder S, Gehrke AR, Bulyk ML, Hughes TR, Wodak SJ. Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences. Nucleic Acids Research. 38: 7927-42. PMID 20705649 DOI: 10.1093/nar/gkq714  1
2010 On T, Xiong X, Pu S, Turinsky A, Gong Y, Emili A, Zhang Z, Greenblatt J, Wodak SJ, Parkinson J. The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins. 78: 2075-89. PMID 20455264 DOI: 10.1002/prot.22723  1
2010 Wodak SJ, Janin J. Analytical approximation to the accessible surface area of proteins. Proceedings of the National Academy of Sciences of the United States of America. 77: 1736-40. PMID 16592793 DOI: 10.1073/pnas.77.4.1736  0.32
2009 Fairn GD, Ogata K, Botelho RJ, Stahl PD, Anderson RA, De Camilli P, Meyer T, Wodak S, Grinstein S. An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis. The Journal of Cell Biology. 187: 701-14. PMID 19951917 DOI: 10.1083/jcb.200909025  1
2008 Pu S, Ronen K, Vlasblom J, Greenblatt J, Wodak SJ. Local coherence in genetic interaction patterns reveals prevalent functional versatility. Bioinformatics (Oxford, England). 24: 2376-83. PMID 18718945 DOI: 10.1093/bioinformatics/btn440  1
2007 Janin J, Wodak S. The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007. Structure (London, England : 1993). 15: 755-9. PMID 17637336 DOI: 10.1016/j.str.2007.06.007  1
2007 Pu S, Vlasblom J, Emili A, Greenblatt J, Wodak SJ. Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics. 7: 944-60. PMID 17370254 DOI: 10.1002/pmic.200600636  1
2006 Billingsley G, Santhiya ST, Paterson AD, Ogata K, Wodak S, Hosseini SM, Manisastry SM, Vijayalakshmi P, Gopinath PM, Graw J, Héon E. CRYBA4, a novel human cataract gene, is also involved in microphthalmia. American Journal of Human Genetics. 79: 702-9. PMID 16960806 DOI: 10.1086/507712  1
2006 Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, ... ... Wodak SJ, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 440: 637-43. PMID 16554755 DOI: 10.1038/nature04670  1
2005 Güldener U, Münsterkötter M, Kastenmüller G, Strack N, van Helden J, Lemer C, Richelles J, Wodak SJ, García-Martínez J, Pérez-Ortín JE, Michael H, Kaps A, Talla E, Dujon B, André B, et al. CYGD: The Comprehensive Yeast Genome Database Nucleic Acids Research. 33. PMID 15608217 DOI: 10.1093/nar/gki053  1
2005 Jaramillo A, Wodak SJ. Computational protein design is a challenge for implicit solvation models. Biophysical Journal. 88: 156-71. PMID 15377512 DOI: 10.1529/biophysj.104.042044  1
2004 Simonis N, van Helden J, Cohen GN, Wodak SJ. Transcriptional regulation of protein complexes in yeast. Genome Biology. 5: R33. PMID 15128447 DOI: 10.1186/gb-2004-5-5-r33  1
2004 Simonis N, Wodak SJ, Cohen GN, van Helden J. Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics (Oxford, England). 20: 2370-9. PMID 15073004 DOI: 10.1093/bioinformatics/bth252  1
2003 Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins. 52: 2-9. PMID 12784359 DOI: 10.1002/prot.10381  1
2003 Wernisch L, Wodak SJ. Identifying structural domains in proteins. Methods of Biochemical Analysis. 44: 365-85. PMID 12647395  0.4
2003 Govaerts C, Bondue A, Springael JY, Olivella M, Deupi X, Le Poul E, Wodak SJ, Parmentier M, Pardo L, Blanpain C. Activation of CCR5 by chemokines involves an aromatic cluster between transmembrane helices 2 and 3. The Journal of Biological Chemistry. 278: 1892-903. PMID 12411445 DOI: 10.1074/jbc.M205685200  1
2003 Ogata K, Jaramillo A, Cohen W, Briand JP, Connan F, Choppin J, Muller S, Wodak SJ. Automatic sequence design of major histocompatibility complex class I binding peptides impairing CD8+ T cell recognition. The Journal of Biological Chemistry. 278: 1281-90. PMID 12411444 DOI: 10.1074/jbc.M206853200  1
2002 Wodak SJ, Janin J. Structural basis of macromolecular recognition. Advances in Protein Chemistry. 61: 9-73. PMID 12461820 DOI: 10.1016/S0065-3233(02)61001-0  1
2002 Janin J, Wodak SJ. Protein modules and protein-protein interaction. Introduction. Advances in Protein Chemistry. 61: 1-8. PMID 12461819 DOI: 10.1016/S0065-3233(02)61000-9  1
2002 Jaramillo A, Wernisch L, Héry S, Wodak SJ. Folding free energy function selects native-like protein sequences in the core but not on the surface. Proceedings of the National Academy of Sciences of the United States of America. 99: 13554-9. PMID 12368470 DOI: 10.1073/pnas.212068599  1
2001 Jaramillo A, Wernisch L, Hery S, Wodak SJ. Automatic procedures for protein design. Combinatorial Chemistry & High Throughput Screening. 4: 643-59. PMID 11812260  1
2001 Nadassy K, Tomás-Oliveira I, Alberts I, Janin J, Wodak SJ. Standard atomic volumes in double-stranded DNA and packing in protein--DNA interfaces. Nucleic Acids Research. 29: 3362-76. PMID 11504874 DOI: 10.1093/NAR/29.16.3362  1
2001 Das U, Chen S, Fuxreiter M, Vaguine AA, Richelle J, Berman HM, Wodak SJ. Checking nucleic acid crystal structures. Acta Crystallographica. Section D, Biological Crystallography. 57: 813-28. PMID 11375501 DOI: 10.1107/S0907444901003936  1
1999 Morel N, Bon S, Greenblatt HM, Van Belle D, Wodak SJ, Sussman JL, Massoulié J, Silman I. Effect of mutations within the peripheral anionic site on the stability of acetylcholinesterase. Molecular Pharmacology. 55: 982-92. PMID 10347238 DOI: 10.1124/mol.55.6.982  1
1999 Nadassy K, Wodak SJ, Janin J. Structural features of protein-nucleic acid recognition sites Biochemistry. 38: 1999-2017. PMID 10026283 DOI: 10.1021/bi982362d  1
1996 Kocher JP, Prévost M, Wodak SJ, Lee B. Properties of the protein matrix revealed by the free energy of cavity formation. Structure (London, England : 1993). 4: 1517-29. PMID 8994976 DOI: 10.1016/S0969-2126(96)00157-8  0.4
1996 Gray PM, Kemp GJ, Rawlings CJ, Brown NP, Sander C, Thornton JM, Orengo CM, Wodak SJ, Richelle J. Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium. Trends in Biochemical Sciences. 21: 251-6. PMID 8755246 DOI: 10.1016/0968-0004(96)10037-2  1
1995 Pugliese L, Prevost M, Wodak SJ. Unfolding simulations of the 85-102 β-hairpin of barnase Journal of Molecular Biology. 251: 432-447. PMID 7650741 DOI: 10.1006/jmbi.1995.0446  1
1993 Janin J, Wodak SJ. The quaternary structure of carbonmonoxy hemoglobin Ypsilanti Proteins: Structure, Function and Genetics. 15: 1-4. PMID 8451234 DOI: 10.1002/prot.340150102  1
1993 Cerf C, Lippens G, Muyldermans S, Segers A, Ramakrishnan V, Wodak SJ, Hallenga K, Wyns L. Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: sequential assignment and secondary structure. Biochemistry. 32: 11345-51. PMID 8218199  1
1992 Van Tilbeurgh H, Jenkins J, Chiadmi M, Janin J, Wodak SJ, Mrabet NT, Lambeir AM. Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 3. Changing metal specificity and the pH profile by site- directed mutagenesis Biochemistry. 31: 5467-5471. PMID 1610793 DOI: 10.1021/bi00139a007  1
1992 Lambeir AM, Lauwereys M, Stanssens P, Mrabet NT, Snauwaert J, Van Tilbeurgh H, Matthyssens G, Lasters I, De Maeyer M, Wodak SJ, Jenkins J, Chiadmi M, Janin J. Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 2. Site-directed mutagenesis of the xylose binding site Biochemistry. 31: 5459-5466. PMID 1610792 DOI: 10.1021/bi00139a006  1
1992 Jenkins J, Janin J, Rey F, Chiadmi M, Van Tilbeurgh H, Lasters I, De Maeyer M, Van Belle D, Wodak SJ, Lauwereys M, Stanssens P, Mrabet NT, Snauwaert J, Matthyssens G, Lambeir AM. Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 1. Crystallography and site-directed mutagenesis of metal binding sites Biochemistry. 31: 5449-5458. PMID 1610791 DOI: 10.1021/bi00139a005  1
1991 Prevost M, Wodak SJ, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase. Proceedings of the National Academy of Sciences of the United States of America. 88: 10880-4. PMID 1961758 DOI: 10.1073/pnas.88.23.10880  1
1991 Karplus M, Prévost M, Tidor B, Wodak S. Simulation analysis of the stability mutants R96H of bacteriophage T4 lysozyme and I96A of barnase. Ciba Foundation Symposium. 161: 63-74. PMID 1814697 DOI: 10.1002/9780470514146.ch5  1
1991 Prévost M, Wodak S, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability : molecular dynamics simulations of the lie → Ala mutation in Barnase Journal De Chimie Physique. 88: 2727-2728. DOI: 10.1051/jcp/1991882727  0.4
1988 Rey F, Jenkins J, Janin J, Lasters I, Alard P, Claessens M, Matthyssens G, Wodak S. Structural analysis of the 2.8 A model of Xylose isomerase from Actinoplanes missouriensis Proteins. 4: 165-172. PMID 3237716 DOI: 10.1002/PROT.340040303  1
1987 Van Belle D, Couplet I, Prevost M, Wodak SJ. Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles. Journal of Molecular Biology. 198: 721-35. PMID 3430627 DOI: 10.1016/0022-2836(87)90213-0  0.32
1987 Wodak SJ, De Crombrugghe M, Janin J. Computer studies of interactions between macromolecules Progress in Biophysics and Molecular Biology. 49: 29-63. PMID 3310103 DOI: 10.1016/0079-6107(87)90008-3  1
1985 Janin J, Wodak SJ. Reaction pathway for the quaternary structure change in hemoglobin. Biopolymers. 24: 509-26. PMID 3986294 DOI: 10.1002/bip.360240307  0.52
1983 Janin J, Wodak SJ. Structural domains in proteins and their role in the dynamics of protein function. Progress in Biophysics and Molecular Biology. 42: 21-78. PMID 6353481 DOI: 10.1016/0079-6107(83)90003-2  0.6
1982 Wodak SJ, Janin J. Location of structural domains in protein. Biochemistry. 20: 6544-52. PMID 7306523 DOI: 10.1021/BI00526A005  0.72
1979 Janin J, Wodak S. Conformation of amino acid side-chains in proteins. Journal of Molecular Biology. 125: 357-86. PMID 731698 DOI: 10.1016/0022-2836(78)90408-4  0.76
1979 Wodak SJ, Janin J. Computer analysis of protein-protein interaction. Journal of Molecular Biology. 124: 323-42. PMID 712840 DOI: 10.1016/0022-2836(78)90302-9  0.8
1975 Levinthal C, Wodak SJ, Kahn P, Dadivanian AK. Hemoglobin interaction in sickle cell fibers. I: Theoretical approaches to the molecular contacts. Proceedings of the National Academy of Sciences of the United States of America. 72: 1330-4. PMID 1055409  1
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