2022
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PDBe-KB: collaboratively defining the biological context of structural data
Nucleic Acids Research 50, D534-D542 (2022).
[Article]. Bio2Byte involvement: Pathmanaban Ramasamy, Wim Vranken,
Prediction of Disordered Regions in Proteins with Recurrent Neural Networks and Protein DynamicsJournal of Molecular Biology 434, 0 (2022).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
Panoramic Perspective on Human PhosphositesJournal of Proteome Research 21, 1894-1915 (2022).
[Article]. Bio2Byte involvement: Pathmanaban Ramasamy, Wim Vranken,
Challenges in describing the conformation and dynamics of proteins with ambiguous behaviorFrontiers in Molecular Biosciences 9, 959956 (2022).
[Article]. Bio2Byte involvement: Pathmanaban Ramasamy, Wim Vranken, Jose Gavaldá-García, Joel Roca Martinez, Bhawna Dixit, Maité Sanchez Fornaris, Konstantina Tzavella, David Bickel,
Evolutionary adaptation of the protein folding pathway for secretabilityEMBO Journal n/a, e111344 (2022).
[Article]. Bio2Byte involvement: Wim Vranken,
2021
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Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM
Nature Methods 18, 60-68 (2021).
[Article]. Bio2Byte involvement: Wim Vranken,
MobiDB: Intrinsically disordered proteins in 2021Nucleic Acids Research 49, D361-D367 (2021).
[Article]. Bio2Byte involvement: Pathmanaban Ramasamy, Wim Vranken,
Computational resources for identifying and describing proteins driving liquid-liquid phase separationBriefings in bioinformatics 22, 0 (2021).
[Article]. Bio2Byte involvement: Wim Vranken,
Online biophysical predictions for SARS-CoV-2 proteinsBMC Molecular and Cell Biology 22, bbaa408 (2021).
[Article]. Bio2Byte involvement: Pathmanaban Ramasamy, Wim Vranken, Jose Gavaldá-García, Joel Roca Martinez,
Critical assessment of protein intrinsic disorder predictionNature Methods 18, 472-481 (2021).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
B2bTools: Online predictions for protein biophysical features and their conservationNucleic Acids Research 49, W52-W59 (2021).
[Article]. Bio2Byte involvement: François Ancien, Gabriele Orlando, Wim Vranken, Jose Gavaldá-García, Joel Roca Martinez, Konstantina Tzavella, Daniele Raimondi,
Interpreting a black box predictor to gain insights into early folding mechanismsComputational and Structural Biotechnology Journal 19, 4919-4930 (2021).
[Article]. Bio2Byte involvement: Wim Vranken,
2020
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PDBE-KB: A community-driven resource for structural and functional annotations
Nucleic Acids Research 48, D344-D353 (2020).
[Article]. Bio2Byte involvement: Wim Vranken,
DisProt: Intrinsic protein disorder annotation in 2020Nucleic Acids Research 48, D269-D276 (2020).
[Article]. Bio2Byte involvement: Wim Vranken,
Accurate prediction of protein beta-aggregation with generalized statistical potentialsBioinformatics 36, 2076-2081 (2020).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered ProteinsBiophysical Journal 118, 2952-2965 (2020).
[Article]. Bio2Byte involvement: Wim Vranken,
ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift valuesNucleic acids research 48, W36-W40 (2020).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full ContextJournal of proteome research 19, 3478-3486 (2020).
[Article]. Bio2Byte involvement: Pathmanaban Ramasamy, Wim Vranken,
2019
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Auto-encoding NMR chemical shifts from their native vector space to a residue-level biophysical index
Nature Communications 10, 0 (2019).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
Author Correction: Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins (Scientific Reports, (2017), 7, 1, (8826), 10.1038/s41598-017-08366-3)Scientific Reports 9, 0 (2019).
[Erratum]. Bio2Byte involvement: Taushif Khan, Gabriele Orlando, Wim Vranken, Daniele Raimondi,
Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensatesBioinformatics 35, 4617-4623 (2019).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
Exploring the limitations of biophysical propensity scales coupled with machine learning for protein sequence analysisScientific Reports 9, 0 (2019).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
Structural basis of the subcellular topology landscape of Escherichia coliFrontiers in Microbiology 10, 1-22 (2019).
[Article]. Bio2Byte involvement: Wim Vranken,
2018
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RINspector: A Cytoscape app for centrality analyses and DynaMine flexibility prediction
Bioinformatics 34, 294-296 (2018).
[Article]. Bio2Byte involvement: Wim Vranken,
MobiDB 3.0: More annotations for intrinsic disorder, conformational diversity and interactions in proteinsNucleic Acids Research 46, D471-D476 (2018).
[Article]. Bio2Byte involvement: Wim Vranken,
AmyPro: A database of proteins with validated amyloidogenic regionsNucleic Acids Research 46, D387-D392 (2018).
[Article]. Bio2Byte involvement: Wim Vranken,
Lexicon visualization library and javascript for scientific data visualizationComputing in Science and Engineering 20, 50-65 (2018).
[Article]. Bio2Byte involvement: François Ancien, Taushif Khan, Ibrahim Tanyalçin, Wim Vranken,
Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteomeScientific Reports 8, 16980 (2018).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time WarpingBioinformatics 34, 3118-3125 (2018).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
2017
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Investigating the Molecular Mechanisms Behind Uncharacterized Cysteine Losses from Prediction of Their Oxidation State
Human Mutation 38, 86-94 (2017).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
DisProt 7.0: A major update of the database of disordered proteinsNucleic Acids Research 45, D219-D227 (2017).
[Article]. Bio2Byte involvement: Wim Vranken,
Seeing the trees through the forest: Sequencebased homo- and heteromeric protein-protein interaction sites prediction using random forestBioinformatics 33, 1479-1487 (2017).
[Article]. Bio2Byte involvement: Wim Vranken,
DEOGEN2: Prediction and interactive visualization of single amino acid variant deleteriousness in human proteinsNucleic Acids Research 45, W201-W206 (2017).
[Article]. Bio2Byte involvement: Gabriele Orlando, Ibrahim Tanyalçin, Wim Vranken, Daniele Raimondi,
Exploring the Sequence-based Prediction of Folding Initiation Sites in ProteinsScientific Reports 7, 8826 (2017).
[Article]. Bio2Byte involvement: Taushif Khan, Gabriele Orlando, Wim Vranken, Daniele Raimondi,
SVM-dependent pairwise HMM: An application to protein pairwise alignmentsBioinformatics 33, 3902-3908 (2017).
[Article]. Bio2Byte involvement: Taushif Khan, Gabriele Orlando, Wim Vranken, Daniele Raimondi,
Corrigendum: DisProt 7.0: a major update of the database of disordered proteinsNucleic acids research 45, D1123-D1124 (2017).
[Erratum]. Bio2Byte involvement:
2016
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Early Folding Events, Local Interactions, and Conservation of Protein Backbone Rigidity
Biophysical Journal 110, 572-583 (2016).
[Article]. Bio2Byte involvement: Wim Vranken, Daniele Raimondi,
Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effectsBioinformatics 32, 1797-1804 (2016).
[Article]. Bio2Byte involvement: Wim Vranken, Daniele Raimondi,
Start2Fold: A database of hydrogen/deuterium exchange data on protein folding and stabilityNucleic Acids Research 44, D429-D434 (2016).
[Article]. Bio2Byte involvement: Wim Vranken,
Observation selection bias in contact prediction and its implications for structural bioinformaticsScientific Reports 6, 36679 (2016).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
2015
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Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements
Bioinformatics 31, 1219-1225 (2015).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
NMR Exchange Format: A unified and open standard for representation of NMR restraint dataNature Structural and Molecular Biology 22, 433-434 (2015).
[Letter]. Bio2Byte involvement: Wim Vranken,
An evolutionary view on Disulfide bond connectivities prediction using phylogenetic trees and a simple cysteine mutation modelPLoS ONE 10, e0131792 (2015).
[Article]. Bio2Byte involvement: Gabriele Orlando, Wim Vranken, Daniele Raimondi,
Analysis of the structural quality of the CASD-NMR 2013 entriesJournal of Biomolecular NMR 62, 527-540 (2015).
[Article]. Bio2Byte involvement: Wim Vranken,
The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013Journal of Biomolecular NMR 62, 413-424 (2015).
[Article]. Bio2Byte involvement: Wim Vranken,
Computational approaches for inferring the functions of intrinsically disordered proteinsFrontiers in Molecular Biosciences 2, 45 (2015).
[Short Survey]. Bio2Byte involvement: Wim Vranken,
2014
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Study of the structural and dynamic effects in the FimH adhesin upon α-D-heptyl mannose binding
Journal of Medicinal Chemistry 57, 1416-1427 (2014).
[Article]. Bio2Byte involvement: Wim Vranken,
Small-angle X-ray scattering- and nuclear magnetic resonance-derived conformational ensemble of the highly flexible antitoxin PaaA2Structure 22, 854-865 (2014).
[Article]. Bio2Byte involvement: Wim Vranken,
The DynaMine webserver: Predicting protein dynamics from sequenceNucleic Acids Research 42, W264-W270 (2014).
[Article]. Bio2Byte involvement: Wim Vranken,
NMR structure validation in relation to dynamics and structure determinationProgress in Nuclear Magnetic Resonance Spectroscopy 82, 27-38 (2014).
[Article]. Bio2Byte involvement: Wim Vranken,
NMR-based modeling and refinement of protein 3D structuresMolecular Modeling of Proteins: Second Edition N/A, 351-380 (2014).
[Chapter]. Bio2Byte involvement:
NMR-based modeling and refinement of protein 3D structuresMolecular Modeling of Proteins: Second Edition N/A, 351-380 (2014).
[Chapter]. Bio2Byte involvement: Wim Vranken,
2013
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Recommendations of the wwPDB NMR validation task force
Structure 21, 1563-1570 (2013).
[Article]. Bio2Byte involvement: Wim Vranken,
Improving 3D structure prediction from chemical shift dataJournal of Biomolecular NMR 57, 27-35 (2013).
[Article]. Bio2Byte involvement: Wim Vranken,
From protein sequence to dynamics and disorder with DynaMineNature Communications 4, 3741 (2013).
[Article]. Bio2Byte involvement: Wim Vranken,
2012
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Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts
Biochemistry 51, 2224-2231 (2012).
[Article]. Bio2Byte involvement: Wim Vranken,
Protein structure validation using side-chain chemical shiftsJournal of Physical Chemistry B 116, 4754-4759 (2012).
[Article]. Bio2Byte involvement: Wim Vranken,
NRG-CING: Integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDBNucleic Acids Research 40, D519–D524 (2012).
[Article]. Bio2Byte involvement: Wim Vranken,
Blind testing of routine, fully automated determination of protein structures from nmr dataStructure 20, 227-236 (2012).
[Article]. Bio2Byte involvement: Wim Vranken,
ACPYPE - AnteChamber PYthon Parser interfacEBMC Research Notes 5, 367 (2012).
[Article]. Bio2Byte involvement: Wim Vranken,
CING: An integrated residue-based structure validation program suiteJournal of Biomolecular NMR 54, 267-283 (2012).
[Article]. Bio2Byte involvement: Wim Vranken,
WeNMR: Structural Biology on the GridJournal of Grid Computing 10, 743-767 (2012).
[Article]. Bio2Byte involvement: Wim Vranken,
2011
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Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures
Proteins: Structure, Function and Bioinformatics 79, 1525-1537 (2011).
[Article]. Bio2Byte involvement: Wim Vranken,
Structure-based prediction of methyl chemical shifts in proteinsJournal of Biomolecular NMR 50, 331-346 (2011).
[Article]. Bio2Byte involvement: Wim Vranken,
Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structuresAngewandte Chemie - International Edition 50, 9620-9623 (2011).
[Article]. Bio2Byte involvement: Wim Vranken,
WeNMR: Structural biology on the gridCEUR Workshop Proceedings 819, 743-767 (2011).
[Conference Paper]. Bio2Byte involvement: Wim Vranken,