VIB-VUB Center for Structural Biology

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Title DOI
https://doi.org/10.1038/nature12506 Richness of human gut microbiome correlates with metabolic markers
https://doi.org/10.1038/nature15766 Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
https://doi.org/10.1016/j.tcb.2018.02.004 Protein Phase Separation: A New Phase in Cell Biology
https://doi.org/10.1038/nphys3532 Polymer physics of intracellular phase transitions
https://doi.org/10.1371/journal.pcbi.1002606 Microbial Co-occurrence Relationships in the Human Microbiome
https://doi.org/10.1038/nbt.2939 Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
https://doi.org/10.1038/s41564-017-0072-8 Enterotypes in the landscape of gut microbial community composition
https://doi.org/10.1016/j.cell.2018.05.057 A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain
https://doi.org/10.1038/nature12735 Activation and allosteric modulation of a muscarinic acetylcholine receptor
https://doi.org/10.1038/nature14886 Structural insights into µ-opioid receptor activation
https://doi.org/10.1038/s41586-020-2829-0 Single-particle cryo-EM at atomic resolution
https://doi.org/10.1038/nature12000 Conformational biosensors reveal GPCR signalling from endosomes
https://doi.org/10.1093/nar/gkae410 The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
https://doi.org/10.1016/j.tibs.2012.08.004 Intrinsically disordered proteins: a 10-year recap
https://doi.org/10.1016/j.molcel.2014.05.032 A Million Peptide Motifs for the Molecular Biologist
https://doi.org/10.1038/s41586-018-0832-5 GABAA receptor signalling mechanisms revealed by structural pharmacology
https://doi.org/10.1016/j.molcel.2017.02.013 Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics
https://doi.org/10.1371/journal.pbio.1001177 A Holistic Approach to Marine Eco-Systems Biology
https://doi.org/10.1038/s41467-017-01103-4 A homologue of the Parkinson’s disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover
https://doi.org/10.1186/gb-2013-14-1-r4 Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
https://doi.org/10.1016/j.tibtech.2014.03.001 Nanobody-based products as research and diagnostic tools
https://doi.org/10.1016/j.mib.2015.04.004 Metagenomics meets time series analysis: unraveling microbial community dynamics
https://doi.org/10.1016/j.cmet.2020.02.003 Ultrasensitive Genetically Encoded Indicator for Hydrogen Peroxide Identifies Roles for the Oxidant in Cell Migration and Mitochondrial Function
https://doi.org/10.1016/j.str.2019.01.003 Allostery in Its Many Disguises: From Theory to Applications
https://doi.org/10.1136/gutjnl-2011-301805 A metagenomic insight into our gut's microbiome
https://doi.org/10.1016/j.cell.2017.12.011 Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor
https://doi.org/10.1038/s41592-021-01117-3 Critical assessment of protein intrinsic disorder prediction
https://doi.org/10.1038/s41586-018-0832-5 GABAA receptor signalling mechanisms revealed by structural pharmacology.
https://doi.org/10.1038/s41586-018-0833-4 Cryo-EM structure of the human α1β3γ2 GABAA receptor in a lipid bilayer
https://doi.org/10.1038/nature18636 Allosteric nanobodies reveal the dynamic range and diverse mechanisms of G-protein-coupled receptor activation
https://doi.org/10.1021/jacs.9b02822 Rapid Covalent-Probe Discovery by Electrophile-Fragment Screening
https://doi.org/10.1038/s41586-019-0881-4 Structural insights into the activation of metabotropic glutamate receptors
https://doi.org/10.1038/nature22972 Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist
https://doi.org/10.1016/j.molcel.2015.05.011 Obg and Membrane Depolarization Are Part of a Microbial Bet-Hedging Strategy that Leads to Antibiotic Tolerance
https://doi.org/10.1016/j.redox.2017.05.007 European contribution to the study of ROS: A summary of the findings and prospects for the future from the COST action BM1203 (EU-ROS)
https://doi.org/10.1016/j.cell.2018.11.025 The Molecular Mechanism of Transport by the Mitochondrial ADP/ATP Carrier
https://doi.org/10.1038/nature13768 Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG
https://doi.org/10.4161/idp.24157 What’s in a name? Why these proteins are intrinsically disordered
https://doi.org/10.1016/j.sbi.2011.03.012 Unstructural biology coming of age
https://doi.org/10.1016/j.neuron.2018.04.021 A Genetically Encoded Biosensor Reveals Location Bias of Opioid Drug Action
https://doi.org/10.1093/nar/gkw1056 DisProt 7.0: a major update of the database of disordered proteins
https://doi.org/10.4161/idp.24360 The alphabet of intrinsic disorder
https://doi.org/10.1093/bioinformatics/btx324 PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization
https://doi.org/10.1093/nar/gkab975 The Eukaryotic Linear Motif resource: 2022 release
https://doi.org/10.1126/science.aao4827 Secreted amyloid-β precursor protein functions as a GABA B R1a ligand to modulate synaptic transmission
https://doi.org/10.1146/annurev-pharmtox-010716-104710 Nanobodies to Study G Protein–Coupled Receptor Structure and Function
https://doi.org/10.1038/nmicrobiol.2016.189 Helicobacter pylori adhesin HopQ engages in a virulence-enhancing interaction with human CEACAMs
https://doi.org/10.1038/nature14680 Propagation of conformational changes during μ-opioid receptor activation
https://doi.org/10.1073/pnas.1309275110 Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain
https://doi.org/10.1016/j.cell.2010.05.039 Allostery and Intrinsic Disorder Mediate Transcription Regulation by Conditional Cooperativity
https://doi.org/10.1093/nar/gkaa1058 MobiDB: intrinsically disordered proteins in 2021
https://doi.org/10.1093/nar/gkz975 DisProt: intrinsic protein disorder annotation in 2020
https://doi.org/10.1073/pnas.1113645108 Structural flexibility of the Gαs α-helical domain in the β 2 -adrenoceptor Gs complex
https://doi.org/10.1038/ismej.2013.59 Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
https://doi.org/10.1002/prot.25215 Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition
https://doi.org/10.1136/gutjnl-2013-306423 Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD
https://doi.org/10.1038/s41586-019-1530-7 Structures of influenza A virus RNA polymerase offer insight into viral genome replication
https://doi.org/10.1038/s41586-022-04974-w ADAR1 prevents autoinflammation by suppressing spontaneous ZBP1 activation
https://doi.org/10.2967/jnumed.112.111021 Synthesis, Preclinical Validation, Dosimetry, and Toxicity of 68Ga-NOTA-Anti-HER2 Nanobodies for iPET Imaging of HER2 Receptor Expression in Cancer
https://doi.org/10.1093/nar/gkx1071 MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins
https://doi.org/10.1038/nature25010 Structures of β-klotho reveal a ‘zip code’-like mechanism for endocrine FGF signalling
https://doi.org/10.1016/j.sbi.2015.08.009 Intrinsically disordered proteins: emerging interaction specialists
https://doi.org/10.1038/nature25971 Molecular nucleation mechanisms and control strategies for crystal polymorph selection
https://doi.org/10.1093/nar/gkz848 PhaSePro: the database of proteins driving liquid–liquid phase separation
https://doi.org/10.1128/mmbr.00009-11 The Universally Conserved Prokaryotic GTPases
https://doi.org/10.1038/s41467-017-01019-z Fructose-1,6-bisphosphate couples glycolytic flux to activation of Ras
https://doi.org/10.1038/s41589-018-0145-x Structural insights into binding specificity, efficacy and bias of a β2AR partial agonist
https://doi.org/10.1093/jxb/erv084 Oxidative post-translational modifications of cysteine residues in plant signal transduction
https://doi.org/10.1136/jitc-2020-001749 Therapeutic depletion of CCR8+ tumor-infiltrating regulatory T cells elicits antitumor immunity and synergizes with anti-PD-1 therapy
https://doi.org/10.1093/nar/gkab1082 DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation
https://doi.org/10.1073/pnas.0902179106 Positive selection identifies an in vivo role for FimH during urinary tract infection in addition to mannose binding
https://doi.org/10.1038/nature24645 Structure of PINK1 in complex with its substrate ubiquitin
https://doi.org/10.1016/j.tim.2015.07.010 Bacterial Amyloid Formation: Structural Insights into Curli Biogensis
https://doi.org/10.1038/nature10109 Crystal structure of the FimD usher bound to its cognate FimC–FimH substrate
https://doi.org/10.1111/j.1432-1033.2004.04220.x The optimization of protein secondary structure determination with infrared and circular dichroism spectra
https://doi.org/10.1038/ncomms14937 Structure and antagonism of the receptor complex mediated by human TSLP in allergy and asthma
https://doi.org/10.1021/bc500111t Site-Specific Labeling of Cysteine-Tagged Camelid Single-Domain Antibody-Fragments for Use in Molecular Imaging
https://doi.org/10.1073/pnas.1411607111 Sulfenome mining in Arabidopsis thaliana
https://doi.org/10.1016/j.str.2008.11.011 Crystal Structure of the N-Terminal Domain of the Secretin GspD from ETEC Determined with the Assistance of a Nanobody
https://doi.org/10.1038/nsmb.3484 Structural basis for GABAA receptor potentiation by neurosteroids
https://doi.org/10.1016/j.jmb.2018.07.010 The Role of Functional Amyloids in Bacterial Virulence
https://doi.org/10.1038/ncomms3741 From protein sequence to dynamics and disorder with DynaMine
https://doi.org/10.1038/nchembio.1364 The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu
https://doi.org/10.1073/pnas.1906768116 Mining for protein S-sulfenylation in Arabidopsis uncovers redox-sensitive sites
https://doi.org/10.1093/nar/gku270 The DynaMine webserver: predicting protein dynamics from sequence
https://doi.org/10.1016/j.molcel.2009.05.025 Rejuvenation of CcdB-Poisoned Gyrase by an Intrinsically Disordered Protein Domain
https://doi.org/10.1093/nar/gkad1058 ELM—the Eukaryotic Linear Motif resource—2024 update
https://doi.org/10.1038/ncomms10239 Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system
https://doi.org/10.1093/nar/gkaa1021 PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins
https://doi.org/10.1038/nature11155 SbsB structure and lattice reconstruction unveil Ca2+ triggered S-layer assembly
https://doi.org/10.1371/journal.ppat.1005744 The Dermis as a Delivery Site of Trypanosoma brucei for Tsetse Flies
https://doi.org/10.1038/s41592-020-01001-6 Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM
https://doi.org/10.1093/jxb/erv044 Cysteines under ROS attack in plants: a proteomics view
https://doi.org/10.1002/prot.25870 Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition
https://doi.org/10.1111/tpj.14345 The Plant PTM Viewer, a central resource for exploring plant protein modifications
https://doi.org/10.1038/nature25010 Structures of β-klotho reveal a 'zip code'-like mechanism for endocrine FGF signalling.
https://doi.org/10.1038/s41587-020-0570-8 A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity
https://doi.org/10.1126/science.aag1006 Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420
https://doi.org/10.1126/science.1222753 Adenylate Cyclases of Trypanosoma brucei Inhibit the Innate Immune Response of the Host
https://doi.org/10.1128/jb.00830-07 Characterization of Phenylpyruvate Decarboxylase, Involved in Auxin Production of Azospirillum brasilense