List of works - Wim F. Vranken

A framework for scientific data modeling and automated software development

scientific article

A global analysis of NMR distance constraints from the PDB.

scientific article

A nomenclature and data model to describe NMR experiments

scientific article

ACPYPE - AnteChamber PYthon Parser interfacE

scientific article published on 23 July 2012

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

article

AmyPro: a database of proteins with validated amyloidogenic regions

scientific article published on 13 October 2017

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

scientific article

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

scientific article published in June 1998

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

scientific article

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

scientific article published on 15 August 2019

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

scientific article published in March 2011

Beyond the ribosome: proteome-wide secretability studies using SECRiFY

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

scientific article

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

scientific article

CASD-NMR: critical assessment of automated structure determination by NMR

scientific article

CING: an integrated residue-based structure validation program suite

scientific article published on 18 September 2012

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

scientific article published on 01 April 2009

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

scientific article published on 8 December 2014

Computational approaches for inferring the functions of intrinsically disordered proteins

scientific article (publication date: 2015)

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

scientific article (publication date: 11 May 1999)

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.

scientific article published on February 1996

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

scientific article published on 12 May 2017

DRESS: a database of REfined solution NMR structures.

scientific article

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

scientific article

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

scientific article

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

scientific article published on 06 March 2012

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

scientific article

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

scientific article published on 13 December 2016

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

scientific article

E-MSD: an integrated data resource for bioinformatics.

scientific article

E-MSD: improving data deposition and structure quality

scientific article

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

scientific article

EUROCarbDB: An open-access platform for glycoinformatics

scientific article

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

scientific article

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

scientific article

From protein sequence to dynamics and disorder with DynaMine

scientific article

Improving 3D structure prediction from chemical shift data

scientific article

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

scientific article published on 26 September 2016

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

scientific article published in Scientific Reports

Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper

scientific article published in 2024

Leucine Motifs Stabilize Residual Helical Structure in Disordered Proteins

scientific article published in 2024

MEMOPS: data modelling and automatic code generation

scientific article

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

scientific article published on 10 November 2017

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

scientific article published on 18 February 2016

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

scientific article

NMR structure validation in relation to dynamics and structure determination.

scientific article

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

scientific article

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

scientific article

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

scientific article published on 18 November 2016

Online biophysical predictions for SARS-CoV-2 proteins

scientific article published on 23 April 2021

PDBe: Protein Data Bank in Europe

scientific article published on 2 November 2010

PDBe: Protein Data Bank in Europe

scientific article published on 21 November 2011

PDBe: Protein Data Bank in Europe

article

Pescador: the PEptides in Solution ConformAtion Database: Online Resource

scientific article

Protein structure validation using side-chain chemical shifts

scientific article

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

scientific article (publication date: June 2005)

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

scientific article published on 22 September 2017

Recommendations of the wwPDB NMR Validation Task Force

scientific article

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

scientific article

Remediation of the protein data bank archive

scientific article

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

scientific article

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

scientific article published on 28 June 2017

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

scientific article published on 10 January 2017

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

scientific article

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

scientific article (publication date: 10 September 2002)

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

scientific article

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

scientific article

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

scientific article

Straightforward and complete deposition of NMR data to the PDBe

scientific article

Structure-based prediction of methyl chemical shifts in proteins

scientific article

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

scientific article

The ACPYPE web server for small-molecule MD topology generation

scientific article published in 2023

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

scientific article (publication date: June 2005)

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

scientific article

The DynaMine webserver: predicting protein dynamics from sequence

scientific article published on 11 April 2014

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 19 April 2018

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

scientific article published on 2 September 2011

Validation of archived chemical shifts through atomic coordinates

scientific article

b2bTools: online predictions for protein biophysical features and their conservation

scientific article published on 01 July 2021

List of works by Wim F. Vranken

A framework for scientific data modeling and automated software development

A global analysis of NMR distance constraints from the PDB.

A nomenclature and data model to describe NMR experiments

ACPYPE - AnteChamber PYthon Parser interfacE

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

AmyPro: a database of proteins with validated amyloidogenic regions

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

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

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

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

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

Beyond the ribosome: proteome-wide secretability studies using SECRiFY

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

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

CASD-NMR: critical assessment of automated structure determination by NMR

CING: an integrated residue-based structure validation program suite

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

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

Computational approaches for inferring the functions of intrinsically disordered proteins

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

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.

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

DRESS: a database of REfined solution NMR structures.

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

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

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

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

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

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

E-MSD: an integrated data resource for bioinformatics.

E-MSD: improving data deposition and structure quality

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

EUROCarbDB: An open-access platform for glycoinformatics

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

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

From protein sequence to dynamics and disorder with DynaMine

Improving 3D structure prediction from chemical shift data

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

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

Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper

Leucine Motifs Stabilize Residual Helical Structure in Disordered Proteins

MEMOPS: data modelling and automatic code generation

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

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

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

NMR structure validation in relation to dynamics and structure determination.

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

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

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

Online biophysical predictions for SARS-CoV-2 proteins

PDBe: Protein Data Bank in Europe

PDBe: Protein Data Bank in Europe

PDBe: Protein Data Bank in Europe

Pescador: the PEptides in Solution ConformAtion Database: Online Resource

Protein structure validation using side-chain chemical shifts

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

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

Recommendations of the wwPDB NMR Validation Task Force

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

Remediation of the protein data bank archive

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

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

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

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

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

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

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

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

Straightforward and complete deposition of NMR data to the PDBe

Structure-based prediction of methyl chemical shifts in proteins

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

The ACPYPE web server for small-molecule MD topology generation

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

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

The DynaMine webserver: predicting protein dynamics from sequence

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

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

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

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