Lista de obras - Wim F. Vranken - Dominio Público Uruguay

A framework for scientific data modeling and automated software development

artículo científico publicado en 2004

A global analysis of NMR distance constraints from the PDB.

artículo científico publicado en 2007

A nomenclature and data model to describe NMR experiments

artículo científico publicado en 2006

ACPYPE - AnteChamber PYthon Parser interfacE

artículo científico publicado en 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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 1998

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

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 2005

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

artículo científico publicado en 2012

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

artículo científico publicado en 2009

CING: an integrated residue-based structure validation program suite

artículo científico publicado en 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

artículo científico publicado en 2014

Computational approaches for inferring the functions of intrinsically disordered proteins

artículo científico publicado en 2015

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

artículo científico publicado en 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.

artículo científico publicado en 1996

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

artículo científico publicado en 2017

DRESS: a database of REfined solution NMR structures.

artículo científico publicado en 2004

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

artículo científico publicado en 2000

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

artículo científico publicado en 2005

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

artículo científico publicado en 2012

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

artículo científico publicado en 1998

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

artículo científico publicado en 2016

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

artículo científico publicado en 2016

E-MSD: an integrated data resource for bioinformatics.

artículo científico publicado en 2004

E-MSD: improving data deposition and structure quality

artículo científico publicado en 2006

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

artículo científico publicado en 2003

EUROCarbDB: An open-access platform for glycoinformatics

artículo científico publicado en 2011

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

artículo científico publicado en 2016

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

artículo científico publicado en 2017

From protein sequence to dynamics and disorder with DynaMine

artículo científico publicado en 2013

Improving 3D structure prediction from chemical shift data

artículo científico publicado en 2013

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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

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

artículo científico publicado en 2024

Leucine Motifs Stabilize Residual Helical Structure in Disordered Proteins

artículo científico publicado en 2024

MEMOPS: data modelling and automatic code generation

artículo científico publicado en 2010

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

NMR structure validation in relation to dynamics and structure determination.

artículo científico publicado en 2014

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

artículo científico publicado en 2015

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

artículo científico publicado en 2011

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

artículo científico publicado en 2016

Online biophysical predictions for SARS-CoV-2 proteins

artículo científico publicado en 2021

PDBe: Protein Data Bank in Europe

artículo científico publicado en 2010

PDBe: Protein Data Bank in Europe

artículo científico publicado en 2011

PDBe: Protein Data Bank in Europe

article

Pescador: the PEptides in Solution ConformAtion Database: Online Resource

artículo científico publicado en 2002

Protein structure validation using side-chain chemical shifts

artículo científico publicado en 2012

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

artículo científico publicado en 2005

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

artículo científico publicado en 2017

Recommendations of the wwPDB NMR Validation Task Force

artículo científico publicado en 2013

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

artículo científico publicado en 2009

Remediation of the protein data bank archive

artículo científico publicado en 2008

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

artículo científico publicado en 2006

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

artículo científico

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2002

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

artículo científico publicado en 2002

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

artículo científico publicado en 2002

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

artículo científico publicado en 2016

Straightforward and complete deposition of NMR data to the PDBe

artículo científico publicado en 2010

Structure-based prediction of methyl chemical shifts in proteins

artículo científico publicado en 2011

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

artículo científico publicado en 2014

The ACPYPE web server for small-molecule MD topology generation

artículo científico publicado en 2023

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

artículo científico publicado en 2005

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

artículo científico publicado en 2002

The DynaMine webserver: predicting protein dynamics from sequence

artículo científico publicado en 2014

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

artículo científico publicado en 2009

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

artículo científico publicado en 1995

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

artículo científico publicado en 2015

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

artículo científico publicado en 2018

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

artículo científico publicado en 2011

Validation of archived chemical shifts through atomic coordinates

artículo científico publicado en 2010

b2bTools: online predictions for protein biophysical features and their conservation

artículo científico publicado en 2021

Lista de obras de 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.