Publications

Found 35 results
Filters: Author is Vranken, Wim F  [Clear All Filters]
2018
Varadi, M., G. De Baets, W. F. Vranken, P. Tompa, and R. Pancsa, "AmyPro: a database of proteins with validated amyloidogenic regions.", Nucleic Acids Res, vol. 46, issue D1, pp. D387-D392, 2018 Jan 04.
Piovesan, D., F. Tabaro, L. Paladin, M. Necci, I. Mičetić, C. Camilloni, N. Davey, Z. Dosztányi, B. Mészáros, A. M. Monzon, et al., "MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins.", Nucleic Acids Res, vol. 46, issue D1, pp. D471-D476, 2018 Jan 04.
2017
Raimondi, D., G. Orlando, J. Messens, and W. F. Vranken, "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
Pancsa, R., M. Varadi, P. Tompa, and W. F. Vranken, "Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability.", Nucleic Acids Res, vol. 44, issue D1, pp. D429-34, 2016 Jan 04.
2015
Vranken, W. F., G. W. Vuister, and A. M. J. J. Bonvin, "NMR-based modeling and refinement of protein 3D structures.", Methods Mol Biol, vol. 1215, pp. 351-80, 2015.
2014
Raimondi, D., G. Orlando, and W. F. Vranken, "Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements.", Bioinformatics, 2014 Dec 8.
Cilia, E., R. Pancsa, P. Tompa, T. Lenaerts, and W. F. Vranken, "The DynaMine webserver: predicting protein dynamics from sequence.", Nucleic Acids Res, vol. 42, issue Web Server issue, pp. W264-70, 2014 Jul.
Vranken, W. F., "NMR structure validation in relation to dynamics and structure determination.", Prog Nucl Magn Reson Spectrosc, vol. 82C, pp. 27-38, 2014 Oct.
Sterckx, Y. G. J., A. Volkov, W. F. Vranken, J. Kragelj, M. Ringkjøbi Jensen, L. Buts, A. Garcia-Pino, T. Jové, L. Van Melderen, M. Blackledge, et al., "Small-angle X-ray scattering- and nuclear magnetic resonance-derived conformational ensemble of the highly flexible antitoxin PaaA2.", Structure, vol. 22, issue 6, pp. 854-65, 2014 Jun 10.
Vanwetswinkel, S., A. Volkov, Y. G. J. Sterckx, A. Garcia-Pino, L. Buts, W. F. Vranken, J. Bouckaert, R. Roy, L. Wyns, and N. A. J. van Nuland, "Study of the structural and dynamic effects in the FimH adhesin upon α-d-heptyl mannose binding.", J Med Chem, vol. 57, issue 4, pp. 1416-27, 2014 Feb 27.
2013
Cilia, E., R. Pancsa, P. Tompa, T. Lenaerts, and W. F. Vranken, "From protein sequence to dynamics and disorder with DynaMine.", Nat Commun, vol. 4, pp. 2741, 2013.
van der Schot, G., Z. Zhang, R. Vernon, Y. Shen, W. F. Vranken, D. Baker, A. M. J. J. Bonvin, and O. F. Lange, "Improving 3D structure prediction from chemical shift data.", J Biomol NMR, vol. 57, issue 1, pp. 27-35, 2013 Sep.
Montelione, G. T., M. Nilges, A. Bax, P. Güntert, T. Herrmann, J. S. Richardson, C. D. Schwieters, W. F. Vranken, G. W. Vuister, D. S. Wishart, et al., "Recommendations of the wwPDB NMR Validation Task Force.", Structure, vol. 21, issue 9, pp. 1563-70, 2013 Sep 3.
2012
da Silva, A. W. Sousa, and W. F. Vranken, "ACPYPE - AnteChamber PYthon Parser interfacE.", BMC Res Notes, vol. 5, pp. 367, 2012.
Rosato, A., J. M. Aramini, C. Arrowsmith, A. Bagaria, D. Baker, A. Cavalli, J. F. Doreleijers, A. Eletsky, A. Giachetti, P. Guerry, et al., "Blind testing of routine, fully automated determination of protein structures from NMR data.", Structure, vol. 20, issue 2, pp. 227-36, 2012 Feb 8.
Doreleijers, J. F., A. W. Sousa da Silva, E. Krieger, S. B. Nabuurs, C. A. E. M. Spronk, T. J. Stevens, W. F. Vranken, G. Vriend, and G. W. Vuister, "CING: an integrated residue-based structure validation program suite.", J Biomol NMR, vol. 54, issue 3, pp. 267-83, 2012 Nov.
Camilloni, C., A. De Simone, W. F. Vranken, and M. Vendruscolo, "Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts.", Biochemistry, vol. 51, issue 11, pp. 2224-31, 2012 Mar 20.
Doreleijers, J. F., W. F. Vranken, C. Schulte, J. L. Markley, E. L. Ulrich, G. Vriend, and G. W. Vuister, "NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.", Nucleic Acids Res, vol. 40, issue Database issue, pp. D519-24, 2012 Jan.
Sahakyan, A. B., A. Cavalli, W. F. Vranken, and M. Vendruscolo, "Protein structure validation using side-chain chemical shifts.", J Phys Chem B, vol. 116, issue 16, pp. 4754-9, 2012 Apr 26.
2011
Bernard, A., W. F. Vranken, B. Bardiaux, M. Nilges, and T. E. Malliavin, "Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures.", Proteins, vol. 79, issue 5, pp. 1525-37, 2011 May.
von der Lieth, C-W., A. Ardá Freire, D. Blank, M. P. Campbell, A. Ceroni, D. R. Damerell, A. Dell, R. A. Dwek, B. Ernst, R. Fogh, et al., "EUROCarbDB: An open-access platform for glycoinformatics.", Glycobiology, vol. 21, issue 4, pp. 493-502, 2011 Apr.
Velankar, S., Y. Alhroub, A. Alili, C. Best, H. C. Boutselakis, S. Caboche, M. J. Conroy, J. M. Dana, G. van Ginkel, A. Golovin, et al., "PDBe: Protein Data Bank in Europe.", Nucleic Acids Res, vol. 39, issue Database issue, pp. D402-10, 2011 Jan.
Sahakyan, A. B., W. F. Vranken, A. Cavalli, and M. Vendruscolo, "Structure-based prediction of methyl chemical shifts in proteins.", J Biomol NMR, vol. 50, issue 4, pp. 331-46, 2011 Aug.
Sahakyan, A. B., W. F. Vranken, A. Cavalli, and M. Vendruscolo, "Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures.", Angew Chem Int Ed Engl, vol. 50, issue 41, pp. 9620-3, 2011 Oct 4.
2010
Fogh, R. H., W. Boucher, J. M. C. Ionides, W. F. Vranken, T. J. Stevens, and E. D. Laue, "MEMOPS: data modelling and automatic code generation.", J Integr Bioinform, vol. 7, issue 3, 2010.

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