Publications

Found 48 results
Filters: Keyword is Computational Biology  [Clear All Filters]
2017
Nguyen, H. Huy, Varadi M., Tompa P., and Pauwels K., "Affinity purification of human m-calpain through an intrinsically disordered inhibitor, calpastatin.", PLoS One, vol. 12, issue 3, pp. e0174125, 2017.
Raimondi, D., Orlando G., Messens J., and Vranken W. F., "Investigating the Molecular Mechanisms Behind Uncharacterized Cysteine Losses from Prediction of Their Oxidation State.", Hum Mutat, vol. 38, issue 1, pp. 86-94, 2017 01.
2016
Vandervelde, A., Loris R., Danckaert J., and Gelens L., "Computational Methods to Model Persistence.", Methods Mol Biol, vol. 1333, pp. 207-40, 2016.
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.
Bhowmick, P., Guharoy M., and Tompa P., "Bioinformatics Approaches for Predicting Disordered Protein Motifs.", Adv Exp Med Biol, vol. 870, pp. 291-318, 2015.
Tusnády, G. E., Dobson L., and Tompa P., "Disordered regions in transmembrane proteins.", Biochim Biophys Acta, vol. 1848, issue 11 Pt A, pp. 2839-48, 2015 Nov.
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.
Habchi, J., Tompa P., Longhi S., and Uversky V. N., "Introducing protein intrinsic disorder.", Chem Rev, vol. 114, issue 13, pp. 6561-88, 2014 Jul 09.
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.
2013
Lensink, M. F., and Wodak S. J., "Docking, scoring, and affinity prediction in CAPRI.", Proteins, vol. 81, issue 12, pp. 2082-95, 2013 Dec.
2012
da Silva, A. W. Sousa, and Vranken W. F., "ACPYPE - AnteChamber PYthon Parser interfacE.", BMC Res Notes, vol. 5, pp. 367, 2012.
Kalmar, L., Acs V., Silhavy D., and Tompa P., "Long-range interactions in nonsense-mediated mRNA decay are mediated by intrinsically disordered protein regions.", J Mol Biol, vol. 424, issue 3-4, pp. 125-31, 2012 Dec 7.
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
von der Lieth, C-W., Freire A. Ardá, Blank D., Campbell M. P., Ceroni A., Damerell D. R., Dell A., Dwek R. A., Ernst B., Fogh R., et al., "EUROCarbDB: An open-access platform for glycoinformatics.", Glycobiology, vol. 21, issue 4, pp. 493-502, 2011 Apr.
Hao, Y., Merkoulovitch A., Vlasblom J., Pu S., Turinsky A. L., Roudeva D., Turner B., Greenblatt J., and Wodak S. J., "OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.", Bioinformatics, vol. 27, issue 6, pp. 883-4, 2011 Mar 15.
Guharoy, M., Pal A., Dasgupta M., and Chakrabarti P., "PRICE (PRotein Interface Conservation and Energetics): a server for the analysis of protein-protein interfaces.", J Struct Funct Genomics, vol. 12, issue 1, pp. 33-41, 2011 Mar.
Schad, E., Tompa P., and Hegyi H., "The relationship between proteome size, structural disorder and organism complexity.", Genome Biol, vol. 12, issue 12, pp. R120, 2011.
Tompa, P., "Unstructural biology coming of age.", Curr Opin Struct Biol, vol. 21, issue 3, pp. 419-25, 2011 Jun.
2010
Lensink, M. F., and Wodak S. J., "Blind predictions of protein interfaces by docking calculations in CAPRI.", Proteins, vol. 78, issue 15, pp. 3085-95, 2010 Nov 15.
De Brakeleer, S., De Grève J., Loris R., Janin N., Lissens W., Sermijn E., and Teugels E., "Cancer predisposing missense and protein truncating BARD1 mutations in non-BRCA1 or BRCA2 breast cancer families.", Hum Mutat, vol. 31, issue 3, pp. E1175-85, 2010 Mar.
Lensink, M. F., and Wodak S. J., "Docking and scoring protein interactions: CAPRI 2009.", Proteins, vol. 78, issue 15, pp. 3073-84, 2010 Nov 15.
Kovacs, E., Tompa P., Liliom K., and Kalmar L., "Dual coding in alternative reading frames correlates with intrinsic protein disorder.", Proc Natl Acad Sci U S A, vol. 107, issue 12, pp. 5429-34, 2010 Mar 23.
On, T., Xiong X., Pu S., Turinsky A., Gong Y., Emili A., Zhang Z., Greenblatt J., Wodak S. J., and Parkinson J., "The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses.", Proteins, vol. 78, issue 9, pp. 2075-89, 2010 Jul.
Pu, S., Turinsky A. L., Vlasblom J., On T., Xiong X., Emili A., Zhang Z., Greenblatt J., Parkinson J., and Wodak S. J., "Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human.", PLoS One, vol. 5, issue 11, pp. e14122, 2010.
Turner, B., Razick S., Turinsky A. L., Vlasblom J., Crowdy E. K., Cho E., Morrison K., Donaldson I. M., and Wodak S. J., "iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence.", Database (Oxford), vol. 2010, pp. baq023, 2010.

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