W. Vranken

发表

Recommendations of the wwPDB NMR Validation Task Force.

G. Montelione, D. Wishart, A. Bax, 2013, Structure.

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

M. Nilges, T. Malliavin, W. Vranken, 2011, Proteins.

Validation of archived chemical shifts through atomic coordinates

W. Vranken, W. Rieping, 2010, Proteins.

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

Y. Moreau, M. Rooman, T. Lenaerts, 2018, Scientific Reports.

Distance-based metrics for comparing conformational ensembles of intrinsically disordered proteins

S. Wodak, P. Tompa, W. Vranken, 2020, bioRxiv.

DisProt 7.0: a major update of the database of disordered proteins

Sonia Longhi, Silvio C. E. Tosatto, Arne Elofsson, 2016, Nucleic Acids Res..

DisProt: intrinsic protein disorder annotation in 2020

Silvio C. E. Tosatto, Arne Elofsson, Marco Necci, 2019, Nucleic Acids Res..

Online biophysical predictions for SARS-CoV-2 proteins

K. Feenstra, W. Vranken, L. Kagami, 2021, BMC molecular and cell biology.

Online biophysical predictions for SARS-CoV-2 proteins

K. Feenstra, W. Vranken, L. Kagami, 2020, bioRxiv.

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

W. Vranken, J. Tanha, F. Ni, 2002, Biochemistry.

Structural Basis of the Subcellular Topology Landscape of Escherichia coli

S. Karamanou, F. Rousseau, W. Vranken, 2019, Front. Microbiol..

Computational approaches for inferring the functions of intrinsically disordered proteins

P. Tompa, W. Vranken, M. Guharoy, 2015, Front. Mol. Biosci..

Progress in Nuclear Magnetic Resonance Spectroscopy

W. Vranken, Wim F. Vranken, 2014 .

Protein structure validation using side-chain chemical shifts.

Aleksandr B. Sahakyan, A. Cavalli, M. Vendruscolo, 2012, The journal of physical chemistry. B.

CING: an integrated residue-based structure validation program suite

Gert Vriend, Tim J. Stevens, Wim F. Vranken, 2012, Journal of Biomolecular NMR.

Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins.

S. Wodak, P. Tompa, W. Vranken, 2020, Biophysical journal.

Prediction of disordered regions in proteins with recurrent Neural Networks and protein dynamics.

W. Vranken, Francesco Tabaro, D. Raimondi, 2022, Journal of molecular biology.

Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

S. Degroeve, W. De Neve, N. Callewaert, 2020, Nature Communications.

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

Daniele Raimondi, Joris Messens, Wim F Vranken, 2017, Human mutation.

Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM

E. Pardon, J. Steyaert, W. Vranken, 2019, Nature Methods.

An intrinsically disordered proteins community for ELIXIR

Silvio C. E. Tosatto, Richard J. Edwards, Norman E. Davey, 2019, F1000Research.

EUROCarbDB: An open-access platform for glycoinformatics

Martin Frank, René Ranzinger, Wim F Vranken, 2010, Glycobiology.

Deep mutational scanning of essential bacterial proteins can guide antibiotic development

J. Michiels, Nandini Krishnamurthy, W. Vranken, 2022, bioRxiv.

An intrinsically disordered proteins community for ELIXIR [version 1; peer review: 2 approved]

Richard J. Edwards, Philippe Le Mercier, J. M. Hancock, 2020 .

PDBe: Protein Data Bank in Europe

Ingvar C. Lagerstedt, Alan W. Sousa da Silva, Robert A. Slowley, 2010, Nucleic Acids Res..

MIADE metadata guidelines: Minimum Information About a Disorder Experiment

Silvio C. E. Tosatto, Norman E. Davey, J. Hoch, 2022, bioRxiv.

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

W. Vranken, F. Ni, P. Xu, 1999, Biochemistry.

Challenges in describing the conformation and dynamics of proteins with ambiguous behavior

W. Vranken, R. Pancsa, I. Grau, 2022, Frontiers in Molecular Biosciences.

Evolutionary adaptation of the protein folding pathway for secretability

S. Karamanou, W. Vranken, A. Vorobieva, 2022, The EMBO journal.

Prediction of disordered regions in proteins with recurrent Neural Networks and protein dynamics

W. Vranken, Francesco Tabaro, D. Raimondi, 2020, bioRxiv.

Evolution of CRISPR-associated endonucleases as inferred from resurrected proteins

J. A. Gavira, W. Vranken, B. Kleinstiver, 2022, bioRxiv.

DisProt 7.0: a major update of the database of disordered proteins

Daniel B. Roche, Damiano Piovesan, A. Dunker, 2016, Nucleic Acids Res..

DisProt 7.0: a major update of the database of disordered proteins

Daniel B. Roche, Damiano Piovesan, A. Dunker, 2016, Nucleic acids research.

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 β‐hairpins

W. Vranken, F. Ni, H. Bennett, 2002 .

Deep mutational scanning of essential bacterial proteins can guide antibiotic development

J. Michiels, Nandini Krishnamurthy, W. Vranken, 2022, bioRxiv.

Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria

G. Rodrigo, W. Vranken, J. Buijs, 2022, bioRxiv.

WeNMR: Structural Biology on the Grid

H. Schwalbe, G. Vriend, P. Güntert, 2011, Journal of Grid Computing.

CING: an integrated residue-based structure validation program suite

G. Vriend, E. Krieger, S. Nabuurs, 2012, Journal of biomolecular NMR.

PDBe-KB: a community-driven resource for structural and functional annotations

Alfonso Valencia, Karel Berka, Jaroslav Koča, 2019, Nucleic Acids Res..

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

Wayne Boucher, Wim F Vranken, John L Markley, 2005, Proteins.

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

Bin Wu, Antonio Rosato, Gaohua Liu, 2015, Journal of biomolecular NMR.

Blind testing of routine, fully automated determination of protein structures from NMR data.

Harald Schwalbe, Bin Wu, David Baker, 2012, Structure.

ACPYPE - AnteChamber PYthon Parser interfacE

Wim F Vranken, Alan W Sousa da Silva, W. Vranken, 2012, BMC Research Notes.

E-MSD: an integrated data resource for bioinformatics

Sameer Velankar, Geoffrey J. Barton, John G. Tate, 2004, Nucleic Acids Res..

The DynaMine webserver: predicting protein dynamics from sequence

Tom Lenaerts, Peter Tompa, Wim F. Vranken, 2014, Nucleic Acids Res..

Structure-based prediction of methyl chemical shifts in proteins

Aleksandr B. Sahakyan, A. Cavalli, M. Vendruscolo, 2011, Journal of biomolecular NMR.

MutaFrame—an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome

F. Pucci, M. Rooman, W. Vranken, 2021, bioRxiv.

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

Tom Lenaerts, Julien Ferté, Andrea Gazzo, 2017, Nucleic Acids Res..

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

Tom Lenaerts, Daniele Raimondi, Wim F. Vranken, 2016, Bioinform..

PDBe: Protein Data Bank in Europe

Sameer Velankar, Swanand P. Gore, Gerard J. Kleywegt, 2011, Nucleic acids research.

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

Yves Moreau, Daniele Raimondi, Gabriele Orlando, 2018, Bioinform..

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

Y. Moreau, M. Rooman, T. Lenaerts, 2018, Scientific Reports.

A framework for scientific data modeling and automated software development

T. N. Bhat, John D. Westbrook, Tim J. Stevens, 2005, Bioinform..

Evolutionary adaptation of the folding pathway for secretability

S. Karamanou, W. Vranken, A. Vorobieva, 2022, bioRxiv.

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

T. N. Bhat, Gary Gilliland, Michael Nilges, 2002, Nature Structural Biology.

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

Silvio C. E. Tosatto, Marco Necci, Damiano Piovesan, 2017, Nucleic Acids Res..

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

W. Vranken, F. Ni, D. Tolkatchev, 2000, Biochemistry.

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.

W. Vranken, F. Ni, P. Xu, 1999, The journal of peptide research : official journal of the American Peptide Society.

A panoramic perspective on human phosphosites

W. Vranken, L. Martens, E. Vandermarliere, 2022, bioRxiv.

AmyPro: a database of proteins with validated amyloidogenic regions

Peter Tompa, Wim F. Vranken, Rita Pancsa, 2017, Nucleic Acids Res..

Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts.

Carlo Camilloni, Michele Vendruscolo, Wim F Vranken, 2012, Biochemistry.

Seeing the trees through the forest: sequence‐based homo‐ and heteromeric protein‐protein interaction sites prediction using random forest

Jaap Heringa, Wim F. Vranken, K. Anton Feenstra, 2016, Bioinform..

Critical assessment of protein intrinsic disorder prediction

M. Y. Lobanov, David C. Jones, K. Paliwal, 2021, Nature Methods.

MobiDB: intrinsically disordered proteins in 2021

Silvio C. E. Tosatto, Marco Necci, Damiano Piovesan, 2020, Nucleic Acids Res..

Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM

E. Pardon, J. Steyaert, J. Naismith, 2021, Nature Methods.

PDBe-KB: collaboratively defining the biological context of structural data

Roland L. Dunbrack, Thomas A. Hopf, Leandro G. Radusky, 2021, Nucleic Acids Res..

Deciphering the RRM-RNA recognition code: A computational analysis

W. Vranken, M. Sattler, Joel Roca-Martínez, 2023, PLoS computational biology.

Computational resources for identifying and describing proteins driving liquid–liquid phase separation

W. Vranken, R. Pancsa, Bálint Mészáros, 2021, Briefings Bioinform..

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

Charles A Laughton, Modesto Orozco, Wim Vranken, 2009, Proteins.

WeNMR: Structural Biology on the Grid

Dmitri I. Svergun, Stefano Dal Pra, Torsten Herrmann, 2011, Journal of Grid Computing.

Scop3P: a comprehensive resource of human phosphosites within their full context.

W. Vranken, L. Martens, E. Vandermarliere, 2020, Journal of proteome research.

Scop3P: a comprehensive resource of human phosphosites within their full context

Lennart Martens, Niels Hulstaert, Wim F. Vranken, 2019, bioRxiv.

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

Li Xueli, Wayne Boucher, David I Stuart, 2004, Proteins.

From protein sequence to dynamics and disorder with DynaMine

Tom Lenaerts, Wim F Vranken, Peter Tompa, 2013, Nature Communications.

What stabilizes pre-folded structures in the intrinsically disordered α-helical binding motifs?

W. Vranken, S. Hadži, Uroš Zavrtanik, 2022, bioRxiv.

PDBe: Protein Data Bank in Europe

Sameer Velankar, Gerard J. Kleywegt, Wim F. Vranken, 2009, Nucleic Acids Res..

Accurate prediction of protein beta-aggregation with generalized statistical potentials

Alexandra Silva, Daniele Raimondi, Gabriele Orlando, 2019, Bioinform..

Small-angle X-ray scattering- and nuclear magnetic resonance-derived conformational ensemble of the highly flexible antitoxin PaaA2.

Wim F Vranken, Remy Loris, Martin Blackledge, 2014, Structure.

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

W. Vranken, A. C. Storer, N. Goudreau, 1998, FEBS letters.

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

Daniele Raimondi, Wim F Vranken, Elisa Cilia, 2016, Biophysical journal.

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

Miron Livny, Michael Nilges, Alexandre M J J Bonvin, 2005, Proteins.

Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins.

Michele Vendruscolo, Wim Vranken, Andrea Cavalli, 2009, Journal of the American Chemical Society.

Remediation of the protein data bank archive

Haruki Nakamura, Zukang Feng, John D. Westbrook, 2007, Nucleic Acids Res..

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

Yves Moreau, Daniele Raimondi, Gabriele Orlando, 2019, Bioinform..

E-MSD: improving data deposition and structure quality

Sameer Velankar, John G. Tate, Wim F. Vranken, 2005, Nucleic Acids Res..

E-MSD: an integrated data resource for bioinformatics.

Rolf Apweiler, Sameer Velankar, A. Suarez, 2004, Nucleic acids research.

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

W. Vranken, F. Borremans, F. Fant, 1999, Proteins.

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

Peter Tompa, Wim F. Vranken, Rita Pancsa, 2015, Nucleic Acids Res..

ACPYPE - AnteChamber PYthon Parser

Wim F. Vranken, W Sousa da Silva, W. Vranken, 2012 .

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

Sameer Velankar, John G. Tate, Wim F. Vranken, 2003, Nucleic Acids Res..

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

A. Rachedi, R. J. Morris, C. Cambillau, 2006, Acta crystallographica. Section D, Biological crystallography.

Interpreting a black box predictor to gain insights into early folding mechanisms

A. Nowé, W. Vranken, I. Grau, 2021, Computational and structural biotechnology journal.

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

W. Vranken, R. Pancsa, D. Raimondi, 2017, Scientific Reports.

BMC Structural Biology BioMed Central

Wolfgang Rieping, Wim F Vranken, W. Vranken, 2009 .

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

Zhenbao Yu, W. Vranken, F. Ni, 2002, Biochemistry.

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

G. Montelione, A. Rosato, W. Vranken, 2015, Journal of biomolecular NMR.

DRESS: a database of REfined solution NMR structures

Alexandre M J J Bonvin, Gert Vriend, Jurgen F Doreleijers, 2004, Proteins.

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

Alexandre M J J Bonvin, Jurgen F Doreleijers, Wim Vranken, 2005, Journal of biomolecular NMR.

Exploring the limitations of biophysical propensity scales coupled with machine learning for protein sequence analysis

Yves Moreau, Daniele Raimondi, Gabriele Orlando, 2019, Scientific Reports.

Improving 3D structure prediction from chemical shift data

Oliver F. Lange, David Baker, Yang Shen, 2013, Journal of biomolecular NMR.

NMR structure validation in relation to dynamics and structure determination.

W. Vranken, 2014, Progress in nuclear magnetic resonance spectroscopy.

NMR-based modeling and refinement of protein 3D structures.

Alexandre M J J Bonvin, Wim F Vranken, Geerten W Vuister, 2015, Methods in molecular biology.

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

W. Vranken, M. Buděšínský, F. Borremans, 2001, European journal of biochemistry.

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

K. Boulez, W. Vranken, M. Buděšínský, 1995, FEBS letters.

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

Michael Nilges, Sameer Velankar, Torsten Herrmann, 2015, Nature Structural &Molecular Biology.

SVM‐dependent pairwise HMM: an application to protein pairwise alignments

Tom Lenaerts, Daniele Raimondi, Wim F Vranken, 2017, Bioinform..

Improving 3D structure prediction from chemical shift data

R. Vernon, W. Vranken, A. Bonvin, 2013, Journal of Biomolecular NMR.

e-NMR gLite grid enabled infrastructure

Andrea Giachetti, Harald Schwalbe, Torsten Herrmann, 2010 .

Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures.

Aleksandr B. Sahakyan, A. Cavalli, M. Vendruscolo, 2011, Angewandte Chemie.

Straightforward and complete deposition of NMR data to the PDBe

Sameer Velankar, Gerard J. Kleywegt, Tim J. Stevens, 2010, Journal of biomolecular NMR.

A nomenclature and data model to describe NMR experiments

Tim J. Stevens, Wayne Boucher, Wim F. Vranken, 2006, Journal of biomolecular NMR.

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.

K. Boulez, W. Vranken, H. Gras-masse, 1996, European journal of biochemistry.

New simulation insights on the structural transition mechanism of bovine rhodopsin activation

W. Vranken, C. Sudandiradoss, Taushif Khan, 2023, Proteins.

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

G. Orlando, D. Raimondi, W. F. Vranken, 2016, Scientific Reports.

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

Marc F. Lensink, Wim F. Vranken, Guillaume Brysbaert, 2017, Bioinform..

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

L. Wyns, W. Vranken, A. Garcia-Pino, 2014, Journal of medicinal chemistry.

Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

S. Degroeve, N. Callewaert, W. Vranken, 2021, Nature Communications.

Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

S. Degroeve, N. Callewaert, W. Vranken, 2018, bioRxiv.

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

W. Vranken, W. Broekaert, F. Borremans, 1998, Journal of molecular biology.

The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries

John L. Markley, Gert Vriend, Wim F. Vranken, 2009, Journal of biomolecular NMR.

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

Daniele Raimondi, Wim F Vranken, Gabriele Orlando, 2017, Scientific Reports.

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

Silvio C. E. Tosatto, M. Y. Lobanov, Md. Wasi Ul Kabir, 2023, Nucleic Acids Res..

PESCADOR: The PEptides in Solution ConformAtion Database: Online Resource

S. Wodak, W. Vranken, M. Jiménez, 2002, Journal of biomolecular NMR.

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

John L. Markley, Gert Vriend, Wim F. Vranken, 2011, Nucleic Acids Res..

Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria

G. Rodrigo, W. Vranken, J. Buijs, 2023, bioRxiv.

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

M. Nilges, T. Malliavin, W. Vranken, 2011, Proteins.

Panoramic Perspective on Human Phosphosites.

W. Vranken, L. Martens, E. Vandermarliere, 2022, Journal of proteome research.

Blind testing of routine, fully automated determination of protein structures from NMR data.

Oliver F. Lange, Gaohua Liu, G. Montelione, 2012, Structure.

MEMOPS: Data modelling and automatic code generation

Tim J. Stevens, Wayne Boucher, Wim F. Vranken, 2010, J. Integr. Bioinform..

b2bTools: online predictions for protein biophysical features and their conservation

W. Vranken, D. Raimondi, L. Kagami, 2021, Nucleic Acids Res..

ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values

W. Vranken, D. Raimondi, L. Kagami, 2020, Nucleic Acids Res..

A global analysis of NMR distance constraints from the PDB

Wim Vranken, W. Vranken, 2007, Journal of biomolecular NMR.