Bio2Byte publications

Year 2025 (4 publications)

Article

GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design

Journal of Molecular Biology 437, 169164 (2025)

DOI: 10.1016/j.jmb.2025.169164

Bio2Byte involvement:

Adrian Diaz, Charlotte Crauwels, Wim Vranken

Article

Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics

Journal of Molecular Biology 437, 168900 (2025)

DOI: 10.1016/j.jmb.2024.168900

Bio2Byte involvement:

Jose Gavaldá-García, Bhawna Dixit, Adrian Diaz, Wim Vranken

Article

Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep

Briefings in Bioinformatics 26, bbae664 (2025)

DOI: 10.1093/bib/bbae664

Bio2Byte involvement:

Konstantina Tzavella, Adrian Diaz, Wim Vranken

Article

Critical assessment of missense variant effect predictors on disease-relevant variant data

Human Genetics 144, 281-293 (2025)

DOI: 10.1007/s00439-025-02732-2

Bio2Byte involvement:

François Ancien, Wim Vranken Daniele Raimondi

Year 2024 (7 publications)

Article

Bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties

Bioinformatics 40, btae543 (2024)

DOI: 10.1093/bioinformatics/btae543

Bio2Byte involvement:

Jose Gavaldá-García, Adrian Diaz, Wim Vranken

Article

Data-driven probabilistic definition of the low energy conformational states of protein residues

NAR Genomics and Bioinformatics 6, lqae082 (2024)

DOI: 10.1093/nargab/lqae082

Bio2Byte involvement:

Gabriele Orlando, Jose Gavaldá-García, Joel Roca Martinez, David Bickel, Wim Vranken Daniele Raimondi

Article

Effects of Phosphorylation on Protein Backbone Dynamics and Conformational Preferences

Journal of Chemical Theory and Computation 20, 4998-5011 (2024)

DOI: 10.1021/acs.jctc.4c00206

Bio2Byte involvement:

David Bickel, Wim Vranken

Article

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

Bioinformatics 40, btae276 (2024)

DOI: 10.1093/bioinformatics/btae276

Bio2Byte involvement:

Adrian Diaz, Charlotte Crauwels, Sophie-Luise Heidig, Wim Vranken

Article

Analysis of the inter-domain orientation of tandem RRM domains with diverse linkers: connecting experimental with AlphaFold2 predicted models

NAR Genomics and Bioinformatics 6, lqae002 (2024)

DOI: 10.1093/nargab/lqae002

Bio2Byte involvement:

Joel Roca Martinez, Wim Vranken

Article

Leucine Motifs Stabilize Residual Helical Structure in Disordered Proteins

Journal of Molecular Biology 436, 168444 (2024)

DOI: 10.1016/j.jmb.2024.168444

Bio2Byte involvement:

Wim Vranken

Article

Conformational dynamics of α-1 acid glycoprotein (AGP) in cancer: A comparative study of glycosylated and unglycosylated AGP

Proteins: Structure, Function and Bioinformatics 92, 246-264 (2024)

DOI: 10.1002/prot.26607

Bio2Byte involvement:

Bhawna Dixit, Wim Vranken

Year 2023 (10 publications)

Erratum

Author Correction: Deep mutational scanning of essential bacterial proteins can guide antibiotic development (Nature Communications, (2023), 14, 1, (241), 10.1038/s41467-023-35940-3)

Nature Communications 14, 657 (2023)

DOI: 10.1038/s41467-023-36287-5

Bio2Byte involvement:

Wim Vranken

Article

Deep mutational scanning of essential bacterial proteins can guide antibiotic development

Nature Communications 14, 241 (2023)

DOI: 10.1038/s41467-023-35940-3

Bio2Byte involvement:

Wim Vranken

Article

The ACPYPE web server for small-molecule MD topology generation

Bioinformatics 39, btad350 (2023)

DOI: 10.1093/bioinformatics/btad350

Bio2Byte involvement:

Adrian Diaz, Wim Vranken Luciano Kagami

Article

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

Proteins: Structure, Function and Bioinformatics 91, 771-780 (2023)

DOI: 10.1002/prot.26465

Bio2Byte involvement:

Taushif Khan, David Bickel, Wim Vranken

Article

Experiences with a training DSW knowledge model for early-stage researchers

Open Research Europe 3, 97 (2023)

DOI: 10.12688/openreseurope.15609.1

Bio2Byte involvement:

Jose Gavaldá-García, Joel Roca Martinez, Wim Vranken

Article

Deciphering the RRM-RNA recognition code: A computational analysis

PLoS Computational Biology 19, e1010859 (2023)

DOI: 10.1371/journal.pcbi.1010859

Bio2Byte involvement:

Joel Roca Martinez, Wim Vranken

Article

Evolution of CRISPR-associated endonucleases as inferred from resurrected proteins

Nature Microbiology 8, 77-90 (2023)

DOI: 10.1038/s41564-022-01265-y

Bio2Byte involvement:

Adrian Diaz, Wim Vranken

Erratum

Author Correction: Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit (Nature Communications, (2021), 12, 1, (6414), 10.1038/s41467-021-26720-y)

Nature Communications 14, 1072 (2023)

DOI: 10.1038/s41467-023-36844-y

Bio2Byte involvement:

Wim Vranken, Pathmanaban Ramasamy

Article

Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions

Nature Methods 20, 1291-1303 (2023)

DOI: 10.1038/s41592-023-01915-x

Bio2Byte involvement:

Kim Van Roey, Wim Vranken

Article

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

Nucleic Acids Research 51, W62-W69 (2023)

DOI: 10.1093/nar/gkad430

Bio2Byte involvement:

Adrian Diaz, Haochen Li, Wim Vranken

Year 2022 (6 publications)

Article

Evolutionary adaptation of the protein folding pathway for secretability

EMBO Journal 41, e111344 (2022)

DOI: 10.15252/embj.2022111344

Bio2Byte involvement:

Wim Vranken

Article

Panoramic Perspective on Human Phosphosites

Journal of Proteome Research 21, 1894-1915 (2022)

DOI: 10.1021/acs.jproteome.2c00164

Bio2Byte involvement:

Wim Vranken, Pathmanaban Ramasamy

Article

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

Frontiers in Molecular Biosciences 9, 959956 (2022)

DOI: 10.3389/fmolb.2022.959956

Bio2Byte involvement:

Jose Gavaldá-García, Joel Roca Martinez, Maité Sanchez Fornaris, David Bickel, Bhawna Dixit, Konstantina Tzavella, Wim Vranken, Pathmanaban Ramasamy

Article

Prediction of Disordered Regions in Proteins with Recurrent Neural Networks and Protein Dynamics

Journal of Molecular Biology 434, 167579 (2022)

DOI: 10.1016/j.jmb.2022.167579

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

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

Bioinformatics 38, 265-266 (2022)

DOI: 10.1093/bioinformatics/btab453

Bio2Byte involvement:

François Ancien, Wim Vranken

Article

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

Nucleic Acids Research 50, D534-D542 (2022)

DOI: 10.1093/nar/gkab988

Bio2Byte involvement:

Wim Vranken, Pathmanaban Ramasamy Gurdeep Singh

Year 2021 (9 publications)

Article

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

Nucleic Acids Research 48, W36-W40 (2021)

DOI: 10.1093/NAR/GKAA391

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi, Luciano Kagami

Article

Online biophysical predictions for SARS-CoV-2 proteins

BMC Molecular and Cell Biology 22, bbaa408 (2021)

DOI: 10.1186/s12860-021-00362-w

Bio2Byte involvement:

Jose Gavaldá-García, Joel Roca Martinez, Wim Vranken, Pathmanaban Ramasamy Luciano Kagami

Review

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

Briefings in Bioinformatics 22, bbaa408 (2021)

DOI: 10.1093/bib/bbaa408

Bio2Byte involvement:

Wim Vranken

Article

B2bTools: Online predictions for protein biophysical features and their conservation

Nucleic Acids Research 49, W52-W59 (2021)

DOI: 10.1093/nar/gkab425

Bio2Byte involvement:

François Ancien, Gabriele Orlando, Jose Gavaldá-García, Joel Roca Martinez, Bhawna Dixit, Konstantina Tzavella, Wim Vranken, Pathmanaban Ramasamy Daniele Raimondi, Luciano Kagami

Article

MobiDB: Intrinsically disordered proteins in 2021

Nucleic Acids Research 49, D361-D367 (2021)

DOI: 10.1093/nar/gkaa1058

Bio2Byte involvement:

Wim Vranken, Pathmanaban Ramasamy

Article

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

Computational and Structural Biotechnology Journal 19, 4919-4930 (2021)

DOI: 10.1016/j.csbj.2021.08.041

Bio2Byte involvement:

Wim Vranken

Article

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

Nature Communications 12, 6414 (2021)

DOI: 10.1038/s41467-021-26720-y

Bio2Byte involvement:

Wim Vranken, Pathmanaban Ramasamy

Article

Critical assessment of protein intrinsic disorder prediction

Nature Methods 18, 472-481 (2021)

DOI: 10.1038/s41592-021-01117-3

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

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

Nature Methods 18, 60-68 (2021)

DOI: 10.1038/s41592-020-01001-6

Bio2Byte involvement:

Aitor Sánchez, Wim Vranken

Year 2020 (5 publications)

Article

Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context

Journal of Proteome Research 19, 3478-3486 (2020)

DOI: 10.1021/acs.jproteome.0c00306

Bio2Byte involvement:

Wim Vranken, Pathmanaban Ramasamy

Article

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

Biophysical Journal 118, 2952-2965 (2020)

DOI: 10.1016/j.bpj.2020.05.015

Bio2Byte involvement:

Wim Vranken

Article

Accurate prediction of protein beta-aggregation with generalized statistical potentials

Bioinformatics 36, 2076-2081 (2020)

DOI: 10.1093/bioinformatics/btz912

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

PDBE-KB: A community-driven resource for structural and functional annotations

Nucleic Acids Research 48, D344-D353 (2020)

DOI: 10.1093/nar/gkz853

Bio2Byte involvement:

Wim Vranken Gurdeep Singh

Article

DisProt: Intrinsic protein disorder annotation in 2020

Nucleic Acids Research 48, D269-D276 (2020)

DOI: 10.1093/nar/gkz975

Bio2Byte involvement:

Wim Vranken

Year 2019 (6 publications)

Article

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

Scientific Reports 9, 16932 (2019)

DOI: 10.1038/s41598-019-53324-w

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Erratum

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, 12140 (2019)

DOI: 10.1038/s41598-019-48219-9

Bio2Byte involvement:

Taushif Khan, Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

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

Nature Communications 10, 2511 (2019)

DOI: 10.1038/s41467-019-10322-w

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

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

Bioinformatics 35, 4617-4623 (2019)

DOI: 10.1093/bioinformatics/btz274

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

Structural basis of the subcellular topology landscape of Escherichia coli

Frontiers in Microbiology 10, 1-22 (2019)

DOI: 10.3389/fmicb.2019.01670

Bio2Byte involvement:

Wim Vranken

Article

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

F1000Research 8, 1753 (2019)

DOI: 10.12688/f1000research.20136.1

Bio2Byte involvement:

Wim Vranken

Year 2018 (6 publications)

Article

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

Bioinformatics 34, 294-296 (2018)

DOI: 10.1093/bioinformatics/btx586

Bio2Byte involvement:

Wim Vranken

Article

AmyPro: A database of proteins with validated amyloidogenic regions

Nucleic Acids Research 46, D387-D392 (2018)

DOI: 10.1093/nar/gkx950

Bio2Byte involvement:

Wim Vranken

Article

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

Scientific Reports 8, 16980 (2018)

DOI: 10.1038/s41598-018-34959-7

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

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

Bioinformatics 34, 3118-3125 (2018)

DOI: 10.1093/bioinformatics/bty309

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

Lexicon visualization library and javascript for scientific data visualization

Computing in Science and Engineering 20, 50-65 (2018)

DOI: 10.1109/MCSE.2018.011111125

Bio2Byte involvement:

François Ancien, Taushif Khan, Ibrahim Tanyalçin, Wim Vranken

Article

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

Nucleic Acids Research 46, D471-D476 (2018)

DOI: 10.1093/nar/gkx1071

Bio2Byte involvement:

Wim Vranken

Year 2017 (7 publications)

Article

SVM-dependent pairwise HMM: An application to protein pairwise alignments

Bioinformatics 33, 3902-3908 (2017)

DOI: 10.1093/bioinformatics/btx391

Bio2Byte involvement:

Taushif Khan, Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

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

Scientific Reports 7, 8826 (2017)

DOI: 10.1038/s41598-017-08366-3

Bio2Byte involvement:

Taushif Khan, Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

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

Nucleic Acids Research 45, W201-W206 (2017)

DOI: 10.1093/nar/gkx390

Bio2Byte involvement:

Gabriele Orlando, Ibrahim Tanyalçin, Wim Vranken Daniele Raimondi

Article

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

Bioinformatics 33, 1479-1487 (2017)

DOI: 10.1093/bioinformatics/btx005

Bio2Byte involvement:

Wim Vranken

Article

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

Nucleic Acids Research 45, D219-D227 (2017)

DOI: 10.1093/nar/gkw1056

Bio2Byte involvement:

Wim Vranken

Article

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

Human Mutation 38, 86-94 (2017)

DOI: 10.1002/humu.23129

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Erratum

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

Nucleic acids research 45, D1123-D1124 (2017)

DOI: 10.1093/nar/gkw1279

Bio2Byte involvement:

Wim Vranken

Year 2016 (4 publications)

Article

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

Scientific Reports 6, 36679 (2016)

DOI: 10.1038/srep36679

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Article

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

Bioinformatics 32, 1797-1804 (2016)

DOI: 10.1093/bioinformatics/btw094

Bio2Byte involvement:

Wim Vranken Daniele Raimondi

Article

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

Biophysical Journal 110, 572-583 (2016)

DOI: 10.1016/j.bpj.2015.12.028

Bio2Byte involvement:

Wim Vranken Daniele Raimondi

Article

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

Nucleic Acids Research 44, D429-D434 (2016)

DOI: 10.1093/nar/gkv1185

Bio2Byte involvement:

Wim Vranken

Year 2015 (6 publications)

Article

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

Journal of Biomolecular NMR 62, 413-424 (2015)

DOI: 10.1007/s10858-015-9953-4

Bio2Byte involvement:

Wim Vranken

Article

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

Journal of Biomolecular NMR 62, 527-540 (2015)

DOI: 10.1007/s10858-015-9949-0

Bio2Byte involvement:

Wim Vranken

Short Survey

Computational approaches for inferring the functions of intrinsically disordered proteins

Frontiers in Molecular Biosciences 2, 45 (2015)

DOI: 10.3389/fmolb.2015.00045

Bio2Byte involvement:

Wim Vranken

Article

An evolutionary view on Disulfide bond connectivities prediction using phylogenetic trees and a simple cysteine mutation model

PLoS ONE 10, e0131792 (2015)

DOI: 10.1371/journal.pone.0131792

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Letter

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

Nature Structural and Molecular Biology 22, 433-434 (2015)

DOI: 10.1038/nsmb.3041

Bio2Byte involvement:

Wim Vranken

Article

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

Bioinformatics 31, 1219-1225 (2015)

DOI: 10.1093/bioinformatics/btu794

Bio2Byte involvement:

Gabriele Orlando, Wim Vranken Daniele Raimondi

Year 2014 (6 publications)

Book Chapter

NMR-based modeling and refinement of protein 3D structures

Molecular Modeling of Proteins: Second Edition N/A, 351-380 (2014)

DOI: 10.1007/978-1-4939-1465-4_16

Bio2Byte involvement:

Wim Vranken

Article

The DynaMine webserver: Predicting protein dynamics from sequence

Nucleic Acids Research 42, W264-W270 (2014)

DOI: 10.1093/nar/gku270

Bio2Byte involvement:

Wim Vranken

Article

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)

DOI: 10.1021/jm401666c

Bio2Byte involvement:

Wim Vranken

Review

NMR structure validation in relation to dynamics and structure determination

Progress in Nuclear Magnetic Resonance Spectroscopy 82, 27-38 (2014)

DOI: 10.1016/j.pnmrs.2014.08.001

Bio2Byte involvement:

Wim Vranken

Chapter

NMR-based modeling and refinement of protein 3D structures

Molecular Modeling of Proteins: Second Edition N/A, 351-380 (2014)

DOI: 10.1007/978-1-4939-1465-4_16

Bio2Byte involvement:

Wim Vranken

Article

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

Structure 22, 854-865 (2014)

DOI: 10.1016/j.str.2014.03.012

Bio2Byte involvement:

Wim Vranken

Year 2013 (3 publications)

Article

From protein sequence to dynamics and disorder with DynaMine

Nature Communications 4, 2741 (2013)

DOI: 10.1038/ncomms3741

Bio2Byte involvement:

Wim Vranken

Article

Recommendations of the wwPDB NMR validation task force

Structure 21, 1563-1570 (2013)

DOI: 10.1016/j.str.2013.07.021

Bio2Byte involvement:

Wim Vranken

Article

Improving 3D structure prediction from chemical shift data

Journal of Biomolecular NMR 57, 27-35 (2013)

DOI: 10.1007/s10858-013-9762-6

Bio2Byte involvement:

Wim Vranken

Year 2012 (7 publications)

Article

WeNMR: Structural Biology on the Grid

Journal of Grid Computing 10, 743-767 (2012)

DOI: 10.1007/s10723-012-9246-z

Bio2Byte involvement:

Wim Vranken

Article

CING: An integrated residue-based structure validation program suite

Journal of Biomolecular NMR 54, 267-283 (2012)

DOI: 10.1007/s10858-012-9669-7

Bio2Byte involvement:

Wim Vranken

Article

ACPYPE - AnteChamber PYthon Parser interfacE

BMC Research Notes 5, 367 (2012)

DOI: 10.1186/1756-0500-5-367

Bio2Byte involvement:

Wim Vranken

Article

Protein structure validation using side-chain chemical shifts

Journal of Physical Chemistry B 116, 4754-4759 (2012)

DOI: 10.1021/jp2122054

Bio2Byte involvement:

Wim Vranken

Article

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

Biochemistry 51, 2224-2231 (2012)

DOI: 10.1021/bi3001825

Bio2Byte involvement:

Wim Vranken

Article

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

Nucleic Acids Research 40, D519–D524 (2012)

DOI: 10.1093/nar/gkr1134

Bio2Byte involvement:

Wim Vranken

Article

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

Structure 20, 227-236 (2012)

DOI: 10.1016/j.str.2012.01.002

Bio2Byte involvement:

Wim Vranken

Year 2011 (4 publications)

Conference Paper

WeNMR: Structural biology on the grid

CEUR Workshop Proceedings 819, 743-767 (2011)

DOI: N/A

Bio2Byte involvement:

Wim Vranken

Article

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

Angewandte Chemie - International Edition 50, 9620-9623 (2011)

DOI: 10.1002/anie.201101641

Bio2Byte involvement:

Wim Vranken

Article

Structure-based prediction of methyl chemical shifts in proteins

Journal of Biomolecular NMR 50, 331-346 (2011)

DOI: 10.1007/s10858-011-9524-2

Bio2Byte involvement:

Wim Vranken

Article

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)

DOI: 10.1002/prot.22980

Bio2Byte involvement:

Wim Vranken