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List of works by Alexandre Bonvin

"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin

scientific article

3D-DART: a DNA structure modelling server

scientific article

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations.

scientific article published on 18 April 2012

A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.

scientific article published on 27 July 2016

A Multidomain Flexible Docking Approach to Deal with Large Conformational Changes in the Modeling of Biomolecular Complexes ⬇️

scientific article published on April 13, 2011

A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking ⬇️

scientific article published on March 13, 2013

A benchmark testing ground for integrating homology modeling and protein docking

scientific article

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

scientific article published on 22 April 2020

A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system

scientific article

A docking approach to the study of copper trafficking proteins; interaction between metallochaperones and soluble domains of copper ATPases.

scientific article published in April 2004

A gp41 MPER-specific Llama VHH Requires a Hydrophobic CDR3 for Neutralization but not for Antigen Recognition

scientific article

A protein-DNA docking benchmark

scientific article

A structure-based benchmark for protein-protein binding affinity

scientific article

ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information

scientific article published in 2024

Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium

scientific article

Adhesion/Growth-Regulatory Galectins: Insights into Their Ligand Selectivity Using Natural Glycoproteins and Glycotopes

scientific article published in 2011

Advances in integrative modeling of biomolecular complexes ⬇️

scientific article published on December 23, 2012

Altered specificity in DNA binding by the lac repressor: a mutant lac headpiece that mimics the gal repressor

scientific article published in September 2005

An enhanced-sampling MD-based protocol for molecular docking

An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45

scientific article published on 30 December 2019

Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against gram-positive pathogenic bacteria

scientific article

Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark

scientific article

Assessment of contact predictions in CASP12: co-evolution and deep learning coming of age.

scientific article published on 26 October 2017

Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120.

scientific article

Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking.

scientific article

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

scientific article published on 25 October 2019

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

scientific article

CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.

scientific article

Characterization and structural analyses of nonspecific lipid transfer protein 1 from mung bean.

scientific article

Characterizing the N- and C-terminal Small ubiquitin-like modifier (SUMO)-interacting motifs of the scaffold protein DAXX.

scientific article

Clustering biomolecular complexes by residue contacts similarity

scientific article published on 8 May 2012

Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a.

scientific article

Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking.

scientific article

Coming to peace with protein complexes? 5th CAPRI evaluation meeting, April 17-19th 2013--Utrecht.

scientific article

Comparative NMR study on the impact of point mutations on protein stability of Pseudomonas mendocina lipase.

scientific article published on 5 July 2006

Computational prediction of protein interfaces: A review of data driven methods

scientific article

Conformational Plasticity of the POTRA 5 Domain in the Outer Membrane Protein Assembly Factor BamA.

scientific article

Conformational Variability of Solution Nucelar Magnetic Resonance Structures

scientific article published on 01 June 1995

Contacts-based prediction of binding affinity in protein-protein complexes

scientific article published on 20 July 2015

Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4

scientific article published on 13 November 2019

Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa

scientific journal article

Cyclization and Docking Protocol for Cyclic Peptide-Protein Modeling Using HADDOCK2.4.

scientific article published on 02 June 2022

DRESS: a database of REfined solution NMR structures.

scientific article

Data publication with the structural biology data grid supports live analysis

scientific article

Data-driven Docking: Using External Information to Spark the Biomolecular Rendez-vous

scientific article published in May 2010

Data-driven docking for the study of biomolecular complexes

scientific article

Data-driven homology modelling of P-glycoprotein in the ATP-bound state indicates flexibility of the transmembrane domains.

scientific article

Deciphering the role of the electrostatic interactions in the alpha-tropomyosin head-to-tail complex

scientific article published in December 2008

DeepRank: a deep learning framework for data mining 3D protein-protein interfaces

scientific article published on 03 December 2021

Defining distance restraints in HADDOCK

scientific article published on 25 June 2018

Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids

scientific article published on 15 June 2016

Defining the limits of homology modeling in information-driven protein docking

scientific article published on 17 October 2013

Describing partially unfolded states of proteins from sparse NMR data

scientific article

Direct NOE refinement of biomolecular structures using 2D NMR data

scientific article

Direct Use of Unassigned Resonances in NMR Structure Calculations with Proxy Residues

scientific article published in June 2006

Direct structure refinement using 3D NOE-NOE spectra of biomolecules

DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes

scientific article published on 29 May 2015

Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification

scientific article published on 30 November 2018

Dynamic control of selectivity in the ubiquitination pathway revealed by an ASP to GLU substitution in an intra-molecular salt-bridge network

scientific article

Editorial overview: Protein-protein interactions

scientific article published on 26 November 2015

Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

scientific article published on 01 October 2021

Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach.

scientific article

Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes.

scientific article published on 9 June 2016

Extended O-GlcNAc on HLA Class-I-Bound Peptides.

scientific article

Faculty of 1000 evaluation for CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

Faculty of 1000 evaluation for GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization

Flexible protein-protein docking

scientific article

Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase

scientific article published on 19 July 2019

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis

scientific article

HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets

scientific article (publication date: December 2007)

HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors.

scientific article

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

scientific article (publication date: 19 February 2003)

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

scientific article published on 28 March 2019

How proteins get in touch: interface prediction in the study of biomolecular complexes.

scientific article published on August 2008

Hydramacin-1, structure and antibacterial activity of a protein from the basal metazoan Hydra

scientific article

Hydration dynamics of the collagen triple helix by NMR.

scientific article published in July 2000

Immunogenicity of Peptide-vaccine Candidates Predicted by Molecular Dynamics Simulations

article

Impaired peroxisome proliferator-activated receptor gamma function through mutation of a conserved salt bridge (R425C) in familial partial lipodystrophy.

scientific article published on 20 February 2007

Importance of lipid-pore loop interface for potassium channel structure and function

scientific article

Improving 3D structure prediction from chemical shift data

scientific article

In support of the BMRB.

scientific article published in September 2012

Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK.

scientific article published in January 2017

Information-driven modeling of large macromolecular assemblies using NMR data

scientific article

Information-driven modeling of protein-peptide complexes

scientific article published in January 2015

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

scientific article

Information-driven structural modelling of protein-protein interactions

scientific article published in January 2015

Inhibition of the integrated stress response by viral proteins that block p-eIF2-eIF2B association

scientific article published on 20 July 2020

Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction.

scientific article published on 13 January 2014

Insight into molecular interactions between two PB1 domains.

scientific article published in March 2004

Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease

scientific article published in March 2009

Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data

scientific article

Integrative Modelling of Biomolecular Complexes

scientific article published on 26 November 2019

Integrative computational modeling of protein interactions

scientific article published on 26 March 2014

Integrative modeling of membrane-associated protein assemblies

scientific article published on 04 December 2020

Intramolecular surface contacts contain information about protein-protein interface regions

scientific article published on 9 June 2006

Kinetics and thermodynamics of type VIII beta-turn formation: a CD, NMR, and microsecond explicit molecular dynamics study of the GDNP tetrapeptide

scientific article

Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODIGY-LIG web server

scientific article published on 01 May 2019

Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK

scientific article published on 10 October 2019

LightDock goes information-driven

scientific article published on 01 February 2020

M3: an integrative framework for structure determination of molecular machines.

scientific article published on 14 August 2017

MINOES: a new approach to select a representative ensemble of structures in NMR studies of (partially) unfolded states. Application to Delta25-PYP.

scientific article

MTMDAT-HADDOCK: high-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry

scientific article

Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis

scholarly article by Winfried Roseboom published in September 2018

Mass spec studio for integrative structural biology.

scientific article

Membrane proteins structures: A review on computational modeling tools.

scientific article published on 14 July 2017

Mode of action of teixobactins in cellular membranes

scientific article published on 05 June 2020

Model for RNA binding and the catalytic site of the RNase Kid of the bacterial parD toxin-antitoxin system.

scientific article published on 27 December 2005

Modeling Antibody-Antigen Complexes by Information-Driven Docking

scientific article published on 11 November 2019

Modeling protein-protein complexes using the HADDOCK webserver "modeling protein complexes with HADDOCK".

scientific article

Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students

scientific article published on 11 January 2016

Molecular dynamics studies of a molecular switch in the glucocorticoid receptor

scientific article published in April 2003

Molecular origins of binding affinity: seeking the Archimedean point ⬇️

scientific article published on July 19, 2013

NMR Relaxation and Internal Dynamics of Ubiquitin from a 0.2 μs MD Simulation

scientific article

NMR Studies of the Human Retinoic Acid Receptor-? DNA-Binding Domain

scientific article published on 01 June 1993

NMR analysis of protein interactions

scientific article

NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist: structural implications for the MHC II (I-Au)-peptide complex from docking calculations

scientific article

NMR resonance assignments of NarE, a putative ADP-ribosylating toxin from Neisseria meningitidis.

scientific article

NMR study of mersacidin and lipid II interaction in dodecylphosphocholine micelles. Conformational changes are a key to antimicrobial activity

scientific article (publication date: 11 April 2003)

NMR-based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids

scientific article published on 2 July 2007

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

scientific article

Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue

scientific article published on 03 August 2021

Natural helix 9 mutants of PPARγ differently affect its transcriptional activity

scientific article published on 16 December 2018

New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies

scientific article

Next challenges in protein-protein docking: from proteome to interactome and beyond

scientific article published on 28 September 2011

Non-interacting surface solvation and dynamics in protein-protein interactions

scientific article published on 21 January 2015

Novel Insights into Guide RNA 5'-Nucleoside/Tide Binding by Human Argonaute 2.

scientific article

Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes

scientific article published in 2008

Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations

scientific article

On the binding affinity of macromolecular interactions: daring to ask why proteins interact ⬇️

scientific article published on December 12, 2012

On the molecular basis of the recognition of angiotensin II (AII). NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131.

scientific article

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

scientific article

PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes

scientific article published on 01 November 2019

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes

scientific article published on 8 August 2016

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.

scientific article

Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

scientific article

Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain

scientific article

Plectasin, a fungal defensin, targets the bacterial cell wall precursor Lipid II.

scientific article

Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems

scientific article published on 03 September 2019

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody.

scientific article published on 28 November 2016

Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR.

scientific article published on 18 May 2015

Protein-protein interactions.

scientific article

Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface.

scientific article published on 25 April 2014

Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3

scientific article published on 20 August 2018

Protein–protein HADDocking using exclusively pseudocontact shifts

scientific article

Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.

scientific article published on 13 May 2010

Quantitative use of chemical shifts for the modeling of protein complexes

scientific article published on 8 July 2011

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

scientific article (publication date: June 2005)

Rapid Prediction of Multi-dimensional NMR Data Sets Using FANDAS.

scientific article published in January 2018

Rapid prediction of multi-dimensional NMR data sets

scientific article

Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C' scalar couplings (3hbJNC')

article

Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator

scientific article

Refinement of protein structures in explicit solvent

scientific article (publication date: 15 February 2003)

SAMPLEX: automatic mapping of perturbed and unperturbed regions of proteins and complexes

scientific article

SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions

scientific article published on 6 June 2012

Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418).

scientific article published in August 2017

Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1.

scientific article

Sequence co-evolution gives 3D contacts and structures of protein complexes

scientific article published on 25 September 2014

Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

scientific article (publication date: September 2000)

Sharing Data from Molecular Simulations

scientific article published on 11 October 2019

Short-chain fatty acids stimulate angiopoietin-like 4 synthesis in human colon adenocarcinoma cells by activating peroxisome proliferator-activated receptor γ

scientific article

Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli

scientific article

Solution structure of the ubiquitin-conjugating enzyme UbcH5B.

scientific article published in November 2004

Solvated docking: introducing water into the modelling of biomolecular complexes.

scientific article

Solvated protein-DNA docking using HADDOCK.

scientific article

Solvated protein-protein docking using Kyte-Doolittle-based water preferences

scientific article published on 24 December 2012

Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes

scientific article

SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots.

scientific article published on 14 August 2017

Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.

scientific article

Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR

scientific article

Structural Determinants of Specific Lipid Binding to Potassium Channels

scientific article published on 4 March 2013

Structural and biochemical characterization of NarE, an iron-containing ADP-ribosyltransferase from Neisseria meningitidis

scientific article

Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.

scientific article

Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.

scientific article

Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.

scientific article

Structure of the DNA-bound BRCA1 C-terminal Region from Human Replication Factor C p140 and Model of the Protein-DNA Complex

scientific article

Structure of the bacterial plant-ferredoxin receptor FusA

scientific article

Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations

scientific article

Supramolecular Organization and Functional Implications of K+  Channel Clusters in Membranes

scientific article published on 7 July 2017

Supramolecular Structure of Membrane-Associated Polypeptides by Combining Solid-State NMR and Molecular Dynamics Simulations

scientific article

Teixobactin kills bacteria by a two-pronged attack on the cell envelope

scientific article published on 3 August 2022

Template-based protein-protein docking exploiting pairwise interfacial residue restraints

scientific article

The C Terminus of Apocytochrome b562 Undergoes Fast Motions and Slow Exchange among Ordered Conformations Resembling the Folded State

scientific article published on 01 April 2002

The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes.

scientific article published on 6 December 2016

The GROMOS96 benchmarks for molecular simulation

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

scientific article

The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail.

scientific article

The alpha-to-beta conformational transition of Alzheimer's Abeta-(1-42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of beta conformation seeding

scientific article

The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics

scientific article

The precision of NMR structure ensembles revisited

scientific article published in March 2003

The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator

scientific article

The solution structure of the AppA BLUF domain: insight into the mechanism of light-induced signaling

scientific article published in January 2006

The solution structure of the human retinoic acid receptor-beta DNA-binding domain

scientific article

The solution structure of the kallikrein-related peptidases inhibitor SPINK6

scientific article

The structural details of the interaction of single-stranded DNA binding protein hSSB2 (NABP1/OBFC2A) with UV-damaged DNA

scientific article published on 30 August 2019

The vancomycin-nisin(1-12) hybrid restores activity against vancomycin resistant Enterococci

scientific article

Time- and ensemble-averaged direct NOE restraints

scientific article published in January 1994

Toward an NMR R factor

article published in 1991

Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II

scientific article (publication date: 2013)

Two-rung Model of a Left-handed β-Helix for Prions Explains Species Barrier and Strain Variation in Transmissible Spongiform Encephalopathies

scientific article published in July 2006

Understanding the role of the Josephin domain in the PolyUb binding and cleavage properties of ataxin-3.

scientific article

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

scientific article

Use of very long-distance NOEs in a fully deuterated protein: an approach for rapid protein fold determination.

scientific article

Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data

scientific article

WHISCY: what information does surface conservation yield? Application to data-driven docking.

scientific article

Water molecules in DNA recognition I: hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy.

scientific article

Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator 1 1Edited by B. Honig ⬇️

scientific article published on October 2, 1998

beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat

scientific article

iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations

scholarly article published 25 May 2018

iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations

scientific article published on 03 December 2018

iScore: A novel graph kernel-based function for scoring protein-protein docking models: Table S1,Table S2

scholarly article published 18 December 2018

iScore: a novel graph kernel-based function for scoring protein-protein docking models

scientific article published on 01 January 2020

pdb-tools: a swiss army knife for molecular structures

article

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