Profile photoWim Vranken
Academic
Department of Bio-engineering Sciences
Informatics and Applied Informatics
Chemistry
Basic (bio-) Medical Sciences
Postal address:
Pleinlaan 2
1050
Brussels
Belgium

Email: Wim.Vranken@vub.be
Phone: +32-2-6291996 (VUB), +32-2-6505943 (IB2)

Expertise

Structural Bioinformatics and computational biology

  • Prediction of biophysical characteristics of proteins from their sequence
  • Effect of amino acid variants on proteins and organisms

Computational aspects of Nuclear Magnetic Resonance (NMR)

  • Statistical analysis of NMR data in relation to protein structure
  • Structure determination of proteins from experimental NMR data

Qualifications

Chemistry, Ph.D., Ugent

1 Dec 199219 Dec 1996

Employment

Academic

Basic (bio-) Medical Sciences

Vrije Universiteit Brussel

Brussels, Belgium

1 Oct 201630 Sep 2021

Academic

Chemistry

Vrije Universiteit Brussel

Brussels, Belgium

1 Oct 201630 Sep 2021

Academic

Informatics and Applied Informatics

Vrije Universiteit Brussel

Brussels, Belgium

1 Oct 201630 Sep 2021

Academic

Department of Bio-engineering Sciences

Vrije Universiteit Brussel

Brussels, Belgium

1 Feb 201230 Sep 2021

Academic

Department of Bio-engineering Sciences

Vrije Universiteit Brussel

Brussels, Belgium

1 Dec 201030 Sep 2016

VUB director

Interuniversity Institute of Bioinformatics in Brussels

Brussels, Belgium

Apr 2014 → …

Maitre d'enseignement

Université Libre de Bruxelles, Faculté des Sciences

Brussels, Belgium

2011 → …

Scientific officer (NMR)

European Bioinformatics Institute, Hinxton

United Kingdom

1 Oct 200130 Sep 2010

Research Fellow

Biotechnology Research Institute, National Research Council, Montreal

Canada

1 Jan 200031 Aug 2001

Postdoctoral researcher

Université Libre de Bruxelles

Brussels, Belgium

1 Jan 199931 Dec 1999

Postdoctoral researcher

Biotechnology Research Institute, National Research Council, Montreal

Canada

1 Jan 199731 Dec 1998

Research output

Auto-encoding NMR chemical shifts from their native vector space to a residue-level biophysical index

Orlando, G., Raimondi, D. & Vranken, W. F., 7 Jun 2019, In : Nature Communications. 10, 9 p.

Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates

Orlando, G., Raimondi, D., Tabaro, F., Codicé, F., Moreau, Y. & Vranken, W., 17 Apr 2019, In : Bioinformatics.

Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome

Raimondi, D., Orlando, G., Tabaro, F., Lenaerts, T., Rooman, M., Moreau, Y. & Vranken, W. F., 19 Nov 2018, In : Scientific Reports. 8, 1, p. 16980 11 p., 16980.

Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome

Raimondi, D., Orlando, G., Tabaro, F., Lenaerts, T., Rooman, M., Moreau, Y. & Vranken, W. F., 16 Nov 2018, In : Scientific Reports. 8, 1, p. 16980 16980.

Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping

Raimondi, D., Orlando, G., Moreau, Y. & Vranken, W. F., 15 Sep 2018, In : Bioinformatics. 34, 18, p. 3118-3125 8 p.

Biophysical validation of fully disordered proteins

Lazar, T., Váradi, M., Vranken, W., Guha Roy, M., Wodak, S. & Tompa, P., 3 Jul 2018.

Biophysical validation of fully disordered proteins

Lazar, T., Varadi, M., Vranken, W., Guha Roy, M., Wodak, S. J. & Tompa, P., 8 Feb 2018.

Lexicon visualization library and javascript for scientific data visualization

Tanyalcin, I., Assaf, C. A., Ferte, J., Ancien, F., Khan, T., Smits, G., Rooman, M. & Vranken, W., 1 Feb 2018, In : Computing in Science and Engineering. 20, 1, p. 50-65 16 p.

RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction

Brysbaert, G., Lorgouilloux, K., Vranken, W. & Lensink, M. F., 15 Jan 2018, In : Bioinformatics. 34, 2, p. 294-296 3 p.

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins

Piovesan, D., Tabaro, F., Paladin, L., Necci, M., Micetic, I., Camilloni, C., Davey, N., Dosztányi, Z., Mészáros, B., Monzon, A. M., Parisi, G., Schad, E., Sormanni, P., Tompa, P., Vendruscolo, M., Vranken, W. F. & Tosatto, S. C. E., 4 Jan 2018, In : Nucleic Acids Research. 46, D1, p. D471-D476 6 p.

SVM-dependent pairwise HMM: an application to Protein pairwise alignments

Orlando, G., Raimondi, D., Khan, T., Lenaerts, T. & Vranken, W., 15 Dec 2017, In : Bioinformatics. 33, 24, p. 3902-3908 7 p.

AmyPro: a database of proteins with validated amyloidogenic regions

Varadi, M., De Baets, G., Vranken, W. F., Tompa, P. & Pancsa, R., 13 Oct 2017, In : Nucleic Acids Research. 46, D1, p. D387-D392 6 p.

Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins

Raimondi, D., Orlando, G., Pancsa, R., Khan, T. & Vranken, W. F., 18 Aug 2017, In : Scientific Reports. 7, 1, p. 8826 11 p., 8826.

DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins

Raimondi, D., Tanyalcin, I., Ferte, J., Gazzo, A., Orlando, G., Lenaerts, T., Rooman, M. & Vranken, W., 3 Jul 2017, In : Nucleic Acids Research. 45, W1, p. W201-W206

Seeing the Trees through the Forest: Sequence-based Homo- and Heteromeric Protein-protein Interaction sites prediction using Random Forest

Hou, Q., De Geest, P., Vranken, W. F., Heringa, J. & Feenstra, K. A., 15 May 2017, In : Bioinformatics. 33, 10, p. 1479-1487 9 p.

DisProt 7.0: a major update of the database of disordered proteins (vol 45, pg D219, 2017): a major update of the database of disordered proteins

Piovesan, D., Tabaro, F., Mičetić, I., Necci, M., Quaglia, F., Oldfield, C. J., Aspromonte, M. C., Davey, N. E., Davidović, R., Dosztányi, Z., Elofsson, A., Gasparini, A., Hatos, A., Kajava, A. V., Kalmar, L., Leonardi, E., Lázár, T., Macedo-Ribeiro, S., Macossay-Castillo, M., Meszaros, A. & 20 othersMinervini, G., Murvai, N., Pujols, J., Roche, D. B., Salladini, E., Schad, E., Schramm, A., Szabo, B., Tantos, A., Tonello, F., Tsirigos, K. D., Veljković, N., Ventura, S., Vranken, W., Warholm, P., Uversky, V. N., Dunker, A. K., Longhi, S., Tompa, P. & Tosatto, S. C. E., 4 Jan 2017, In : Nucleic Acids Research. 45, D1, p. D1123-D1124 9 p.

Observation selection bias in contact prediction and its implications for structural bioinformatics

Orlando, G., Raimondi, D. & Vranken, W. F., 18 Nov 2016, In : Scientific Reports. 6, p. 36679

Investigating the Molecular Mechanisms Behind Uncharacterized Cysteine Losses from Prediction of Their Oxidation State

Raimondi, D., Orlando, G., Messens, J. & Vranken, W. F., 26 Sep 2016, In : Human Mutation. 38, 1, p. 86-94

Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects

Raimondi, D., Gazzo, A. M., Rooman, M., Lenaerts, T. & Vranken, W. F., 15 Jun 2016, In : Bioinformatics. 32, 12, p. 1797-1804

Early Folding Events, Local Interactions, and Conservation of Protein Backbone Rigidity

Pancsa, R., Raimondi, D., Cilia, E. & Vranken, W. F., 2 Feb 2016, In : Biophysical Journal. 110, 3, p. 572-583 12 p.

Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability

Pancsa, R., Váradi, M., Tompa, P. & Vranken, W. F., 2016, In : Nucleic Acids Research. 44, D1, p. D429-D434 6 p.

The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

Rosato, A., Vranken, W., Fogh, R. H., Ragan, T. J., Tejero, R., Pederson, K., Lee, H-W., Prestegard, J. H., Yee, A., Wu, B., Lemak, A., Houliston, S., Arrowsmith, C. H., Kennedy, M., Acton, T. B., Xiao, R., Liu, G., Montelione, G. T. & Vuister, G. W., Aug 2015, In : Journal of Biomolecular NMR. 62, 4, p. 413-424

An Evolutionary View on Disulfide Bond Connectivities Prediction Using Phylogenetic Trees and a Simple Cysteine Mutation Model

Raimondi, D., Orlando, G. & Vranken, W. F., 10 Jul 2015, In : PLoS ONE. 10, 18 p., 7.

Analysis of the structural quality of the CASD-NMR 2013 entries

Ragan, T. J., Fogh, R. H., Tejero, R., Vranken, W., Montelione, G. T., Rosato, A. & Vuister, G. W., 3 Jun 2015, In : Journal of Biomolecular NMR. 62, 4, p. 527-540 14 p.

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

Gutmanas, A., Adams, P. D., Bardiaux, B., Berman, H. M., Case, D. A., Fogh, R. H., Güntert, P., Hendrickx, P. M. S., Herrmann, T., Kleywegt, G. J., Kobayashi, N., Lange, O. F., Markley, J. L., Montelione, G. T., Nilges, M., Ragan, T. J., Schwieters, C. D., Tejero, R., Ulrich, E. L., Velankar, S. & 5 othersVranken, W. F., Wedell, J. R., Westbrook, J., Wishart, D. S. & Vuister, G. W., 3 Jun 2015, In : Nature Structural and Molecular Biology. 22, 6, p. 433-434 2 p.

Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements

Raimondi, D., Orlando, G. & Vranken, W. F., 15 Apr 2015, In : Bioinformatics. 31, 8, p. 1219-1225 7 p.

Computational approaches for inferring the functions of intrinsically disordered proteins

Váradi, M., Vranken, W., Guharoy, M. & Tompa, P., 2015, In : Frontiers in Molecular Biosciences. 2, 8 p., 45.

NMR-based modeling and refinement of protein 3D structures

Vranken, W. F., Vuister, G. W. & Bonvin, A. M. J. J., 2015, Molecular Modeling of Proteins. Kukol, A. (ed.). New York: Springer, p. 351-380 30 p. (Methods in Molecular Biology; vol. 1215).

NMR structure validation in relation to dynamics and structure determination

Vranken, W., Oct 2014, In : Progress in Nuclear Magnetic Resonance Spectroscopy. 82, p. 27-38 11 p.

From protein sequence to dynamics and disorder with DynaMine

Cilia, E., PANCSA, R., Tompa, P., Lenaerts, T. & Vranken, W., 9 Jul 2014, Gordon Research Seminar and Conference, Intrinsically disordered proteins (USA MA, 05.07.2014-11.07.2014), presented as a poster.

Study of the structural and dynamic effects in the FimH adhesin upon α-D-heptyl mannose binding

Vanwetswinkel, S., Volkov, O., Sterckx, Y., Garcia Pino, A., Buts, L., Vranken, W., Bouckaert, J., Roy, R., Wyns, L. & Van Nuland, N., 29 Jan 2014, In : Journal of Medicinal Chemistry. 57, p. 1416-1427 12 p.

Small-Angle X-Ray Scattering- and Nuclear Magnetic Resonance-Derived Conformational Ensemble of the Highly Flexible Antitoxin PaaA2.

Sterckx, Y., Volkov, O., Vranken, W., Kragelj, J., Ringkjøbing Jensen, M., Buts, L., Garcia Pino, A., Jove, T., Van Melderen, L., Blackledge, M., Van Nuland, N. & Loris, R., 2014, In : Structure. 22, 6, p. 854–865 12 p.

The DynaMine webserver: predicting protein dynamics from sequence

Cilia, E., Pancsa, R., Tompa, P., Lenaerts, T. & Vranken, W., 2014, In : Nucleic Acids Research. 42, W1, p. W264-W270

From protein sequence to dynamics and disorder with DynaMine

Cilia, E., PANCSA, R., Tompa, P., Lenaerts, T. & Vranken, W., 9 Dec 2013, BeNeLux Bioinformatics Conference, Brussels 09.12.2013-10.12.2013, presented as a short talk.

From protein sequence to dynamics and disorder with DynaMine

Cilia, E., PANCSA, R., Tompa, P., Lenaerts, T. & Vranken, W., 14 Nov 2013, In : Nature Communications. 4, p. 2741 10 p.

Recommendations of the wwPDB NMR Validation Task Force

Montelione, G., Nilges, M., Bax, A., Güntert, P., Herrmann, T., Richardson, J., Schwieters, C., Vranken, W., Vuister, G., Wishart, D., Berman, H., Kleywegt, G. & Markley, J., 3 Sep 2013, In : Structure. 21, p. 1563-1570 8 p.

Improving 3D structure prediction from chemical shift data.

Van Der Schot, G., Zhang, Z., Vernon, R., Shen, Y., Vranken, W., Baker, D., Bonvin, A. & Lange, O., 3 Aug 2013, In : Journal of Biomolecular NMR. 57, p. 27-35 9 p.

WeNMR: Structural Biology on the Grid

Wassenaar, T., Van Dijk, M., Loureiro-Ferreira, N., Van Der Schot, G., De Vries, S., Schmitz, C., Van Der Zwan, J., Boelens, R., Giachetti, A., Ferella, L., Rosato, A., Bertini, I., Herrmann, T., Jonker, H., Bagaria, A., Jaravine, V., Güntert, P., Schwalbe, H., Vranken, W., Doreleijers, J. & 16 othersVriend, G., Vuister, G., Franke, D., Kikhney, A., Svergun, D., Fogh, R., Ionides, J., Laue, E., Spronk, C., Jurksa, S., Verlato, M., Badoer, S., Dal Pra, S., Mazzucato, M., Frizziero, E. & Bonvin, A., 1 Dec 2012, In : Journal of Grid Computing. 10, p. 743-767 25 p.

CING: an integrated residue-based structure validation program suite

Doreleijers, J., Da Silva, A. W. S., Krieger, E., Nabuurs, S., Spronk, C., Stevens, T., Vranken, W., Vriend, G. & Vuister, G., Nov 2012, In : Journal of Biomolecular NMR. 54, 3, p. 267-283

ACPYPE - AnteChamber PYthon Parser interfacE

Sousa Da Silva, A. & Vranken, W., 23 Jul 2012, In : BMC Research Notes. 5, p. 367 8 p.

Protein Structure Validation Using Side-Chain Chemical Shifts

Sahakyan, A., Cavalli, A., Vranken, W. & Vendruscolo, M., 15 Apr 2012, In : Journal of Physical Chemistry B. 116, p. 4754-4759 6 p.

Determination of Secondary Structure Populations in Disordered States of Proteins Using Nuclear Magnetic Resonance Chemical Shifts

Camilloni, C., De Simone, A., Vranken, W. & Vendruscolo, M., 23 Feb 2012, In : Biochemistry. 51, p. 2224-2231 8 p.

Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

Rosato, A., Aramini, J., Arrowsmith, C., Bagaria, A., Baker, D., Cavalli, A., Doreleijers, J., Eletsky, A., Giachetti, A., Guerry, P., Gutmanas, A., Güntert, P., He, Y., Herrmann, T., Huang, Y., Jaravine, V., Jonker, H., Kennedy, M., Lange, O., Liu, G. & 17 othersMalliavin, T., Mani, R., Mao, B., Montelione, G., Nilges, M., Rossi, P., Van Der Schot, G., Schwalbe, H., Szyperski, T., Vendruscolo, M., Vernon, R., Vranken, W., De Vries, S., Vuister, G., Wu, B., Yang, Y. & Bonvin, A., 8 Feb 2012, In : Structure. 20, p. 227-236 10 p.

PDBe: Protein Data Bank in Europe.

Velankar, S., Alhroub, Y., Best, C., Caboche, S., Conroy, M., Dana, J., Fernandez Montecelo, M., Van Ginkel, G., Golovin, A., Gore, S., Gutmanas, A., Haslam, P., Hendrickx, P. M. S., Heuson, E., Hirshberg, M., John, M., Lagerstedt, I., Mir, S., Newman, L., Oldfield, T. & 12 othersPatwardhan, A., Rinaldi, L., Sahni, G., Sanz-Garcia, E., Sen, S., Slowley, R., Suarez-Uruena, A., Swaminathan, G., Symmons, M., Vranken, W., Wainwright, M. & Kleywegt, G., 21 Nov 2011, In : Nucleic Acids Research. 40, p. 445-452 8 p.

Using Side-Chain Aromatic Proton Chemical Shifts for a Quantitative Analysis of Protein Structures.

Sahakyan, A., Vranken, W., Cavalli, A. & Vendruscolo, M., 4 Oct 2011, In : Angewandte Chemie International Edition. 50, p. 9620-9623 4 p.

Structure-Based Prediction of Methyl Chemical Shifts in Proteins.

Sahakyan, A., Vranken, W., Cavalli, A. & Vendruscolo, M., 12 Jul 2011, In : Journal of Biomolecular NMR. 50, p. 331-346 16 p.

Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures

Bernard, A., Vranken, W., Bardiaux, B., Nilges, M. & Malliavin, T., 6 Jan 2011, In : Proteins: Structure, Function, and Bioinformatics. 79, p. 1525-1537 13 p.

NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.

Doreleijers, J., Vranken, W., Schulte, C., Ulrich, E., Markley, J., Vriend, G. & Vuister, G., 2011, In : Nucleic Acids Research. 40, p. 519-524 6 p.

EUROCarbDB: An open-access platform for glycoinformatics.

Von Der Lieth, C-W., Freire, A. A., Blank, D., Campbell, M., Ceroni, A., Damerell, D., Dell, A., Dwek, R., Ernst, B., Fogh, R., Frank, M., Geyer, H., Geyer, R., Harrison, M., Henrick, K., Herget, S., Hull, W., Ionides, J., Joshi, H., Kamerling, J. & 14 othersLeeflang, B., Lütteke, T., Lundborg, M., Maass, K., Merry, A., Ranzinger, R., Rosen, J., Royle, L., Rudd, P., Schloissnig, S., Stenutz, R., Vranken, W., Widmalm, G. & Haslam, S., 23 Nov 2010, In : Glycobiology. 21, p. 493-502 10 p.

PDBe: Protein Data Bank in Europe

Velankar, S., Alhroub, Y., Alili, A., Best, C., Boutselakis, H., Caboche, S., Conroy, M., Dana, J., Van Ginkel, G., Golovin, A., Gore, S., Gutmanas, A., Haslam, P., Hirshberg, M., John, M., Lagerstedt, I., Mir, S., Newman, L., Oldfield, T., Penkett, C. & 12 othersPinada-Castillo, J., Rinaldi, L., Sahni, G., Sawka, G., Slowley, R., Sousa Da Silva, A., Suarez-Uruena, A., Swaminathan, G., Symmons, M., Vranken, W., Wainwright, M. & Kleywegt, G., 2 Oct 2010, In : Nucleic Acids Research. 39, p. 402-410 9 p.

Straightforward and complete deposition of NMR data to the PDBe.

Penkett, C., Van Ginkel, G., Velankar, S., Swaminathan, G., Ulrich, E., Mading, S., Stevens, T., Fogh, R., Gutmanas, A., Kleywegt, G., Henrick, K. & Vranken, W., 3 Aug 2010, In : Journal of Biomolecular NMR. 48, p. 85-92 8 p.

Validation of archived chemical shifts through atomic coordinates

Rieping, W. & Vranken, W., 28 Apr 2010, In : Proteins: Structure, Function, and Bioinformatics. 78, p. 2482-2489 8 p.

MEMOPS: Data modelling and automatic code generation.

Fogh, R., Boucher, W., Ionides, J., Vranken, W., Stevens, T. & Laue, E., 25 Mar 2010, In : Journal of Integrative Bioinformatics. 7, p. 123 1 p.

PDBe: Protein Data Bank in Europe

Velankar, S., Best, C., Beuth, B., Boutselakis, H., Cobley, N., Sousa Da Silva, A., Dimitropoulos, D., Golovin, A., Hirshberg, M., John, M., Krissinel, E., Newman, R., Oldfield, T., Pajon, A., Penkett, C., Pineda-Castillo, J., Sahni, G., Sen, S., Slowley, R., Suarez-Uruena, A. & 5 othersSwaminathan, G., Van Ginkel, G., Vranken, W., Henrick, K. & Kleywegt, G., 25 Oct 2009, In : Nucleic Acids Research. 38, p. 308-317 10 p.

Highly Accurate Determination of Random Coil Chemical Shifts of Proteins from an Analysis of Loop Regions in Native States

De Simone, A., Cavalli, A., Hsu, S-T. D., Vranken, W. & Vendruscolo, M., 23 Oct 2009, In : Journal of the American Chemical Society. 131, p. 16332-16333 2 p.

The NMR Restraints Grid (NRG) at BMRB for 5,266 protein and nucleic acid PDB entries.

Doreleijers, J., Vranken, W., Schulte, C., Lin, J., Wedell, J., Penkett, C., Vuister, G., Vriend, G., Markley, J. & Ulrich, E., 7 Oct 2009, In : Journal of Biomolecular NMR. 45, p. 389-396 8 p.

CASD-NMR: Critical Assessment of Automated Structure Determination by NMR.

Rosato, A., Bagaria, A., Baker, D., Bardiaux, B., Cavalli, A., Doreleijers, J., Giachetti, A., Guerry, P., Güntert, P., Herrmann, T., Huang, Y., Jonker, H., Mao, B., Malliavin, T., Montelione, G., Nilges, M., Raman, S., Van Der Schot, G., Vranken, W., Vuister, G. & 1 othersBonvin, A., 1 Sep 2009, In : Nature Methods. 6, p. 625-626 2 p.

Relationship between chemical shift value and accessible surface area for all amino acid atoms

Vranken, W. & Rieping, W., 2 Apr 2009, In : BMC Structural Biology. 9, p. 20 1 p.

COCO: A simple tool to enrich the representation of conformational variability in NMR structures.

Laughton, C., Orozco, M. & Vranken, W., 24 Jul 2008, In : Proteins: Structure, Function, and Bioinformatics. 75, p. 206-216 11 p.

Remediation of the protein data bank archive

Henrick, K., Feng, Z., Bluhm, W. F., Dimitropoulos, D., Doreleijers, J. F., Dutta, S., Flippen-Anderson, J. L., Ionides, J., Kamada, C., Krissinel, E., Lawson, C. L., Markley, J. L., Nakamura, H., Newman, R., Shimizu, Y., Swaminathan, J., Velankar, S., Ory, J., Ulrich, E. L., Vranken, W. & 6 othersWestbrook, J., Yamashita, R., Yang, H., Young, J., Yousufuddin, M. & Berman, H. M., Jan 2008, In : Nucleic Acids Research. 36, s1, p. D426-D433

A global analysis of NMR distance constraints from the PDB

Vranken, W., Dec 2007, In : Journal of Biomolecular NMR. 39, 4, p. 303-314 12 p.

A nomenclature and data model to describe NMR experiments

Fogh, R. H., Vranken, W. F., Boucher, W., Stevens, T. J. & Laue, E. D., Nov 2006, In : Journal of Biomolecular NMR. 36, 3, p. 147-155 9 p.

SPINE bioinformatics and data-management aspects of high-throughput structural biology

Albeck, S., Alzari, P., Andreini, C., Banci, L., Berry, I. M., Bertini, I., Cambillau, C., Canard, B., Carter, L., Dym, O., Cohen, S. X., Esnouf, R. M., Felder, C., Ferron, F., Diprose, J. M., Hamer, R., Guillemot, F., Laurent, T., Longhi, S., Lopez, R. & 28 othersBen Jelloul, M., Malet, H., Mochel, T., Morris, R. J., Laskowski, R. A., Luchinat, C., Oinn, T., Pajon, A., Peleg, Y., Poch, O., Perrakis, A., Moulinier, L., Prilusky, J., Ripp, R., Rachedi, A., Rosato, A., Silman, I., Stuart, D. I., Sussman, J. L., Unger, T., Vaughan, B., Thierry, J. C., Vranken, W., Watson, J. D., Thompson, J. D., Thornton, J. M., Whamond, G. & Henrick, K., Oct 2006, In : Acta Crystallographica Section D: Biological Crystallography. 62, 10, p. 1184-1195 12 p.

E-MSD: improving data deposition and structure quality.

Tagari, M., Tate, J., Swaminathan, G. J., Newman, R., Naim, A., Vranken, W., Kapopoulou, A., Hussain, A., Fillon, J., Henrick, K. & Velankar, S., 1 Jan 2006, In : Nucleic acids research.. 34, Database issue, p. D287-290

RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

Nederveen, A. J., Doreleijers, J. F., Vranken, W., Miller, Z., Spronk, C. A. E. M., Nabuurs, S. B., Güntert, P., Livny, M., Markley, J. L., Nilges, M., Ulrich, E. L., Kaptein, R. & Bonvin, A. M. J. J., 1 Jun 2005, In : Proteins. 59, 4, p. 662-672 11 p.

The CCPN data model for NMR spectroscopy: development of a software pipeline

Vranken, W. F., Boucher, W., Stevens, T. J., Fogh, R. H., Pajon, A., Llinas, M., Ulrich, E. L., Markley, J. L., Ionides, J. & Laue, E. D., 1 Jun 2005, In : Proteins. 59, 4, p. 687-696 10 p.

A framework for scientific data modeling and automated software development

Fogh, R. H., Boucher, W., Vranken, W. F., Pajon, A., Stevens, T. J., Bhat, T. N., Westbrook, J., Ionides, J. M. C. & Laue, E. D., 15 Apr 2005, In : Bioinformatics. 21, 8, p. 1678-1684 7 p.

Design of a data model for developing laboratory information management and analysis systems for protein production

Pajon, A., Ionides, J., Diprose, J., Fillon, J., Fogh, R., Ashton, A. W., Berman, H., Boucher, W., Cygler, M., Deleury, E., Esnouf, R., Janin, J., Kim, R., Krimm, I., Lawson, C. L., Oeuillet, E., Poupon, A., Raymond, S., Stevens, T., van Tilbeurgh, H. & 8 othersWestbrook, J., Wood, P., Ulrich, E., Vranken, W., Xueli, L., Laue, E., Stuart, D. I. & Henrick, K., 1 Feb 2005, In : Proteins. 58, 2, p. 278-284 7 p.

BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures

Doreleijers, J. F., Nederveen, A. J., Vranken, W., Lin, J., Bonvin, A. M. J. J., Kaptein, R., Markley, J. L. & Ulrich, E. L., 2005, In : Journal of Biomolecular NMR. 32, 1, p. 1-12 12 p.

E-MSD: An integrated data resource for bioinformatics

Golovin, A., Oldfield, T. J., Tate, J. G., Velankar, S., Barton, G. J., Boutselakis, H., Dmitropoulos, D., Fillon, J., Hussain, A., Ionides, J. M. C., John, M., Keller, P. A., Krissinel, E., McNeil, P., Naim, A., Newman, R., Pajon, A., Pineda, J., Rachedi, A., Copeland, J. & 8 othersSitnov, A., Sobhany, S., Suarez-Uruena, A., Swaminathan, G. J., Tagari, M., Tromm, S., Vranken, W. & Henrick, K., 1 Jan 2004, In : Nucleic Acids Research. 32, DATABASE ISS., p. D211-D216

DRESS: a database of REfined solution NMR structures

Nabuurs, S. B., Nederveen, A. J., Vranken, W., Doreleijers, J. F., Bonvin, A. M. J. J., Vuister, G. W., Vriend, G. & Spronk, C. A. E. M., 2004, In : Proteins. 55, 3, p. 483-486 4 p.

E-MSD: The European Bioinformatics Institute macromolecular structure database

Boutselakis, H., Dimitropoulos, D., Fillon, J., Golovin, A., Henrick, K., Hussain, A., Ionides, J., John, M., Keller, P. A., Krissinel, E., McNeil, P., Naim, A., Newman, R., Oldfield, T., Pineda, J., Rachedi, A., Copeland, J., Sitnov, A., Sobhany, S., Suarez-Uruena, A. & 6 othersSwaminathan, J., Tagari, M., Tate, J., Tromm, S., Velankar, S. & Vranken, W., 1 Jan 2003, In : Nucleic Acids Research. 31, 1, p. 458-462 5 p.

Solution structure and backbone dynamics of the functional cytoplasmic subdomain of human ephrin B2, a cell-surface ligand with bidirectional signaling properties

Song, J., Vranken, W., Xu, P., Gingras, R., Noyce, R. S., Yu, Z., Shen, S-H. & Ni, F., 10 Sep 2002, In : Biochemistry. 41, 36, p. 10942-10949 8 p.

Solution structure of a llama single-domain antibody with hydrophobic residues typical of the VH/VL interface

Vranken, W., Tolkatchev, D., Xu, P., Tanha, J., Chen, Z., Narang, S. & Ni, F., 9 Jul 2002, In : Biochemistry. 41, 27, p. 8570-8579 10 p.

Pescador: the PEptides in Solution ConformAtion Database: Online Resource

Pajon, A., Vranken, W. F., Jimenez, M. A., Rico, M. & Wodak, S. J., Jun 2002, In : Journal of Biomolecular NMR. 23, 2, p. 85-102 18 p.

The CCPN project: an interim report on a data model for the NMR community

Fogh, R., Ionides, J., Ulrich, E., Boucher, W., Vranken, W., Linge, J. P., Habeck, M., Rieping, W., Bhat, T. N., Westbrook, J., Henrick, K., Gilliland, G., Berman, H., Thornton, J., Nilges, M., Markley, J. & Laue, E., Jun 2002, In : Nature Structural Biology. 9, 6, p. 416-418 3 p.

Solution structures of a 30-residue amino-terminal domain of the carp granulin-1 protein and its amino-terminally truncated 3-30 subfragment: implications for the conformational stability of the stack of two beta-hairpins

Vranken, W. F., James, S., Bennett, H. P. J. & Ni, F., 1 Apr 2002, In : Proteins. 47, 1, p. 14-24 11 p.

Conformational model for the consensus V3 loop of the envelope protein gp120 of HIV-1 in a 20% trifluoroethanol/water solution

Vranken, W. F., Fant, F., Budesinsky, M. & Borremans, F. A., 2001, In : European Journal of Biochemistry. 268, 9, p. 2620-2628 9 p.

Design and solution structure of a well-folded stack of two beta-hairpins based on the amino-terminal fragment of human granulin A

Tolkatchev, D., Ng, A., Vranken, W. & Ni, F., 2000, In : Biochemistry. 39, 11, p. 2878-2886 9 p.

The three-dimensional solution structure of Aesculus hippocastanum antimicrobial protein 1 determined by 1H nuclear magnetic resonance

Fant, F., Vranken, W. F. & Borremans, F. A., 15 Nov 1999, In : Proteins. 37, 3, p. 388-403 16 p.

A 30-residue fragment of the carp granulin-1 protein folds into a stack of two beta-hairpins similar to that found in the native protein

Vranken, W. F., Chen, Z. G., Xu, P., James, S., Bennett, H. P. & Ni, F., 1999, In : The Journal of Peptide Research. 53, 5, p. 590-597 8 p.

Conformation of a Cdc42/Rac interactive binding peptide in complex with Cdc42 and analysis of the binding interface

Stevens, W. K., Vranken, W., Goudreau, N., Xiang, H., Xu, P. & Ni, F., 1999, In : Biochemistry. 38, 19, p. 5968-5975 8 p.

An NMR-based identification of peptide fragments mimicking the interactions of the cathepsin B propeptide

Yu, Y., Vranken, W., Goudreau, N., de Miguel, E., Magny, M. C., Mort, J. S., Dupras, R., Storer, A. C. & Ni, F., 5 Jun 1998, In : FEBS Letters. 429, 1, p. 9-16 8 p.

Determination of the three-dimensional solution structure of Raphanus sativus antifungal protein 1 by 1H NMR

Fant, F., Vranken, W., Broekaert, W. & Borremans, F., 1998, In : Journal of Molecular Biology. 279, 1, p. 257-270 14 p.

Conformational features of a synthetic cyclic peptide corresponding to the complete V3 loop of the ELI HIV-1 strain in water

Vranken, W. F., Buděšínský, M., Fant, F., Boulez, K., Gras-Masse, H. & Borremans, F. A. M., May 1996, In : Collection of Czechoslovak Chemical Communications. 61, 5, p. 742-750 9 p.

Conformational features of a synthetic cyclic peptide corresponding to the complete V3 loop of the RF HIV-1 strain in water and water/trifluoroethanol solutions

Vranken, W. F., Budesinsky, M., Martins, J. C., Fant, F., Boulez, K., Gras-Masse, H. & Borremans, F. A., 15 Feb 1996, In : European Journal of Biochemistry. 236, 1, p. 100-108 9 p.

The complete Consensus V3 loop peptide of the envelope protein gp120 of HIV-1 shows pronounced helical character in solution

Vranken, W. F., Budesinsky, M., Fant, F., Boulez, K. & Borremans, F. A., 1995, In : FEBS Letters. 374, 1, p. 117-121 5 p.

ID: 201797