Dr. Alexandre M.J.J. Bonvin

MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Funct...

• Biomolecules
• January 2023

DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Int...

• Bioinformatics
• November 2022

Improving the Quality of Co-evolution Intermolecular Contact Prediction with DisVis

• November 2022

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

• Nature
• August 2022

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

• Journal of Chemical Theory and Computation
• June 2022

Using machine‐learning‐driven approaches to boost hot‐spot's knowledge

• Wiley Interdisciplinary Reviews Computational Molecular Science
• February 2022

Interface refinement of low- to medium-resolution Cryo-EM complexes using HADDOCK2.4

• Structure
• February 2022

A Cyclisation and Docking Protocol for Cyclic Peptide-Protein Modelling using HADDOCK2.4

• January 2022

DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Int...

• December 2021

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

• Nature Communications
• December 2021

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

• Nature Communications
• October 2021

Information-driven modeling of biomolecular complexes

• Current Opinion in Structural Biology
• October 2021

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI ...

• Proteins Structure Function and Bioinformatics
• September 2021

Shape-Restrained Modeling of Protein–Small-Molecule Complexes with High Ambiguity Drive...

• Journal of Chemical Information and Modeling
• August 2021

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

• Journal of Chemical Theory and Computation
• August 2021

Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

• Frontiers in Molecular Biosciences
• July 2021

Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4

• June 2021

50 years of PDB: a catalyst in structural biology

• Nature Methods
• May 2021

Characterization of nucleosome sediments for protein interaction studies by solid-state...

• Magnetic Resonance
• April 2021

Native or non-native protein-protein docking models? Molecular dynamics to the rescue

• April 2021

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

• February 2021

Integrating quantitative proteomics with accurate genome profiling of transcription fac...

• Nucleic Acids Research
• February 2021

MENSAdb: a thorough structural analysis of membrane protein dimers

• Database
• January 2021

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

• Processes
• December 2020

Integrative modeling of membrane-associated protein assemblies

• Nature Communications
• December 2020

Author Correction: Control over the fibrillization yield by varying the oligomeric nucl...

• Communications Chemistry
• November 2020

Control over the fibrillization yield by varying the oligomeric nucleation propensities...

• Communications Chemistry
• November 2020

PDB‐tools web: A user‐friendly interface for the manipulation of ...

• Proteins Structure Function and Bioinformatics
• November 2020

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spe...

• Structure
• October 2020

Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenge...

• Frontiers in Molecular Biosciences
• August 2020

Integrative Modeling of Membrane-associated Protein Assemblies

• July 2020

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

• Nature Microbiology
• July 2020

proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven ...

• Bioinformatics
• July 2020

Mode of action of teixobactins in cellular membranes

• Nature Communications
• June 2020

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bi...

• F1000Research
• April 2020

Biological vs. Crystallographic Protein Interfaces: An Overview of Computational Approa...

• Crystals
• February 2020

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

• Proteins Structure Function and Bioinformatics
• January 2020

A click-flipped enzyme substrate boosts the performance of the diagnostic screening for...

• Chemical Science
• January 2020

Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Ex...

• BIO-PROTOCOL
• January 2020

Coarse-grained (hybrid) integrative modeling of biomolecular interactions

• Computational and Structural Biotechnology Journal
• January 2020

iScore: An MPI supported software for ranking protein–protein docking models based on a...

• SoftwareX
• January 2020

Protein–Protein Modeling Using Cryo-EM Restraints

• January 2020

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrativ...

• Structure
• December 2019

Coupling enhanced sampling of the apo-receptor with template-based ligand conformers se...

• Journal of Computer-Aided Molecular Design
• November 2019

Modeling Antibody-Antigen Complexes by Information-Driven Docking

• Structure
• November 2019

Integrative modelling of biomolecular complexes

• Journal of Molecular Biology
• November 2019

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

• Proteins Structure Function and Bioinformatics
• October 2019

Computational approaches to therapeutic antibody design: established methods and emergi...

• Briefings in Bioinformatics
• October 2019

Sharing Data from Molecular Simulations

• Journal of Chemical Information and Modeling
• October 2019

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

• Journal of Chemical Theory and Computation
• October 2019

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing

• Frontiers in Molecular Biosciences
• October 2019

iScore: an MPI supported software for ranking protein-protein docking models based on a...

• September 2019

The structural details of the interaction of single‐stranded DNA binding protein hSSB2 ...

• Proteins Structure Function and Bioinformatics
• August 2019

Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for...

• Proteins Structure Function and Bioinformatics
• August 2019

LightDock goes information-driven

• Bioinformatics
• August 2019

Less is more: Coarse-grained integrative modeling of large biomolecular assemblies with...

• July 2019

Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Hu...

• ACS Chemical Biology
• June 2019

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

• Bioinformatics
• June 2019

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

• Bioinformatics
• May 2019

LightDock goes information-driven

• April 2019

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

• Journal of Chemical Information and Modeling
• March 2019

Natural helix 9 mutants of PPARγ differently affect its transcriptional activity

• Molecular Metabolism
• February 2019

Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in pro...

• Wiley Interdisciplinary Reviews Computational Molecular Science
• January 2019

West-Life: A Virtual Research Environment for structural biology

• Journal of Structural Biology X
• January 2019

Information-Driven Modelling of Antibody-Antigen Complexes

• SSRN Electronic Journal
• January 2019

A swiss army knife for molecular structures via PDB and mmCIF manipulation

• F1000Research
• December 2018

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

• December 2018

pdb-tools: a swiss army knife for molecular structures

• December 2018

iSEE: Interface structure, evolution, and energy-based machine learning predictor of bi...

• Proteins Structure Function and Bioinformatics
• December 2018

A Membrane Protein Complex Docking Benchmark

• Journal of Molecular Biology
• December 2018

Distinguishing crystallographic from biological interfaces in protein complexes: role o...

• BMC Bioinformatics
• November 2018

An enhanced-sampling MD-based protocol for molecular docking

• October 2018

Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and...

• International Journal of Molecular Sciences
• September 2018

Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODI...

• Bioinformatics
• September 2018

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

• Journal of Computer-Aided Molecular Design
• August 2018

INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures

• Journal of Grid Computing
• August 2018

Defining distance restraints in HADDOCK

• Nature Protocols
• June 2018

iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of bin...

• May 2018

Computational Tools for the Structural Characterization of Proteins and Their Complexes...

• March 2018

Rapid Prediction of Multi-dimensional NMR Data Sets Using FANDAS

• November 2017

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

• Proteins Structure Function and Bioinformatics
• November 2017

Membrane proteins structures: A review on computational modeling tools

• Biochimica et Biophysica Acta (BBA) - Biomembranes
• October 2017

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predi...

• Journal of Computer-Aided Molecular Design
• August 2017

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

• Scientific Reports
• August 2017

M3: an integrative framework for structure determination of molecular machines

• Nature Methods
• August 2017

Supramolecular Organization and Functional Implications of K+  Channel Clusters in Memb...

• Angewandte Chemie International Edition
• August 2017

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

• Proteins Structure Function and Bioinformatics
• July 2017

Abstracts

• European Biophysics Journal
• June 2017

Correction: Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody

• The Journal of Immunology
• April 2017

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

• Journal of Molecular Biology
• February 2017

Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK

• January 2017

Prediction of Biomolecular Complexes

• January 2017

PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes

• BIO-PROTOCOL
• January 2017

Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody

• The Journal of Immunology
• November 2016

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

• Proteins Structure Function and Bioinformatics
• November 2016

A benchmark testing ground for integrating homology modeling and protein docking

• Proteins Structure Function and Bioinformatics
• November 2016

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

• Nature Communications
• November 2016

Structure of the bacterial plant-ferredoxin receptor FusA

• Nature Communications
• October 2016

dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking

• Frontiers in Molecular Biosciences
• August 2016

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

• Bioinformatics
• August 2016

Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-s...

• Journal of Structural Biology
• August 2016

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

• International Journal of Molecular Sciences
• July 2016

Exploring the interplay between experimental methods and the performance of predictors ...

• Protein Engineering Design and Selection
• June 2016

Prediction of homoprotein and heteroprotein complexes by protein docking and template-b...

• Proteins Structure Function and Bioinformatics
• June 2016

New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Doc...

• Journal of Biological Chemistry
• May 2016

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

• Briefings in Bioinformatics
• March 2016

Data publication with the structural biology data grid supports live analysis

• Nature Communications
• March 2016

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

• Journal of Molecular Biology
• February 2016

The solution structure of the kallikrein-related peptidases inhibitor SPINK6

• Biochemical and Biophysical Research Communications
• February 2016

Molecular dynamics characterization of the conformational landscape of small peptides: ...

• Biochemistry and Molecular Biology Education
• January 2016

Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexib...

• Journal of Chemical Information and Modeling
• December 2015

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

• International Journal of Molecular Sciences
• December 2015

Editorial overview: Protein–protein interactions

• Current Opinion in Structural Biology
• December 2015

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

• FEBS Letters
• October 2015

Structure-Function Relationships of Antimicrobial Peptides and Proteins with Respect to...

• Current Topics in Medicinal Chemistry
• September 2015

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Ver...

• Journal of Molecular Biology
• September 2015

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

• Journal of the American Chemical Society
• August 2015

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

• eLife
• July 2015

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

• Structure
• July 2015

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

• Structure
• July 2015

Future opportunities and trends for e-infrastructures and life sciences: going beyond t...

• Frontiers in Genetics
• June 2015

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

• Journal of the American Chemical Society
• June 2015

Faculty of 1000 evaluation for GalaxyPepDock: a protein-peptide docking tool based on i...

• June 2015

Faculty of 1000 evaluation for CABS-dock web server for the flexible docking of peptide...

• June 2015

Dynamic binding mode of a Synaptotagmin-1–SNARE complex in solution

• Nature Structural & Molecular Biology
• June 2015

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

• Bioinformatics
• May 2015

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

• Nature Methods
• May 2015

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

• Journal of Biomolecular NMR
• May 2015

Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscop...

• Structure
• May 2015

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

• Proteins Structure Function and Bioinformatics
• January 2015

Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit

• AIMS Biophysics
• January 2015

Correction: Turning Defense into Offense: Defensin Mimetics as Novel Antibiotics Target...

• PLoS Pathogens
• December 2014

Information-Driven Modeling of Protein-Peptide Complexes

• December 2014

Binding Hotspots of BAZ2B Bromodomain: Histone Interaction Revealed by Solution NMR Dri...

• Biochemistry
• October 2014

Mass Spec Studio for Integrative Structural Biology

• Structure
• October 2014

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

• eLife
• September 2014

NMR-Based Modeling and Refinement of Protein 3D Structures

• September 2014

Information-Driven Structural Modelling of Protein–Protein Interactions

• September 2014

Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the ...

• Journal of Molecular Biology
• July 2014

Information-driven modeling of large macromolecular assemblies using NMR data

• Journal of Magnetic Resonance
• April 2014

Integrative computational modeling of protein interactions

• FEBS Journal
• March 2014

HADDOCK_2P2I: A Biophysical Model for Predicting the Binding Affinity of Prot...

• Journal of Chemical Information and Modeling
• February 2014

Insight into cyanobacterial circadian timing from structural details of the KaiB–KaiC i...

• Proceedings of the National Academy of Sciences
• January 2014

Modeling Protein–Protein Complexes Using the HADDOCK Webserver “Modeling Protein Comple...

• January 2014

Ion Channel - Ion Channel Interaction at Atomic Resolution

• Biophysical Journal
• January 2014

A Single Inter-Domain Salt Bridge within the Human Argonaute 2 Protein Crucially Affect...

• Biophysical Journal
• January 2014

Molecular origins of binding affinity: seeking the Archimedean point

• Current Opinion in Structural Biology
• December 2013

Protein–protein interactions

• Current Opinion in Structural Biology
• December 2013

Blind prediction of interfacial water positions in CAPRI

• Proteins Structure Function and Bioinformatics
• November 2013

Turning Defense into Offense: Defensin Mimetics as Novel Antibiotics Targeting Lipid II

• PLoS Pathogens
• November 2013

Coming to peace with protein complexes? 5thCAPRI evaluation meeting, April 17-19th2013 ...

• Proteins Structure Function and Bioinformatics
• October 2013

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

• Proteins Structure Function and Bioinformatics
• October 2013

Community-wide evaluation of methods for predicting the effect of mutations on protein-...

• Proteins Structure Function and Bioinformatics
• August 2013

Improving 3D structure prediction from chemical shift data

• Journal of Biomolecular NMR
• August 2013

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

• Proceedings of the National Academy of Sciences
• July 2013

Unveiling the Interaction of Vanadium Compounds with Human Serum Albumin by Using1H STD...

• European Journal of Inorganic Chemistry
• July 2013

Solvated protein–DNA docking using HADDOCK

• Journal of Biomolecular NMR
• April 2013

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

• Acta Crystallographica Section D Biological Crystallography
• April 2013

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

• PLoS ONE
• March 2013

A gp41 MPER-specific Llama VHH Requires a Hydrophobic CDR3 for Neutralization but not f...

• PLoS Pathogens
• March 2013

Structural Determinants of Specific Lipid Binding to Potassium Channels

• Journal of the American Chemical Society
• March 2013

Advances in integrative modeling of biomolecular complexes

• Methods
• March 2013

Short-Chain Fatty Acids Stimulate Angiopoietin-Like 4 Synthesis in Human Colon Adenocar...

• Molecular and Cellular Biology
• January 2013

HADDOCK

• January 2013

Gentamicin Binds to the Megalin Receptor as a Competitive Inhibitor Using the Common Li...

• Journal of Biological Chemistry
• December 2012

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

• Proteins Structure Function and Bioinformatics
• December 2012

On the binding affinity of macromolecular interactions: daring to ask why proteins inte...

• Journal of The Royal Society Interface
• December 2012

WeNMR: Structural Biology on the Grid

• Journal of Grid Computing
• November 2012

Rapid prediction of multi-dimensional NMR data sets

• Journal of Biomolecular NMR
• November 2012

Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU ...

• PLoS Computational Biology
• November 2012

In support of the BMRB

• Nature Structural & Molecular Biology
• September 2012

Supramolecular Structure of Membrane-Associated Polypeptides by Combining Solid-State N...

• Biophysical Journal
• July 2012

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

• Journal of Chemical Theory and Computation
• June 2012

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

• Journal of Chemical Theory and Computation
• April 2012

Protein-Protein Docking with HADDOCK

• March 2012

Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR ...

• Structure
• February 2012

Clustering biomolecular complexes by residue contacts similarity

• Proteins Structure Function and Bioinformatics
• January 2012

MTMDAT-HADDOCK: High-throughput, protein complex structure modeling based on limited pr...

• BMC Structural Biology
• January 2012

Antimicrobial activity of carbon nanotubes.

• January 2012

Explicit Treatment of Water Molecules in Data-Driven Protein–Protein Docking: The Solva...

• November 2011

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design...

• Journal of Molecular Biology
• November 2011

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

• Wiley Interdisciplinary Reviews Computational Molecular Science
• September 2011

Quantitative use of chemical shifts for the modeling of protein complexes

• Proteins Structure Function and Bioinformatics
• July 2011

Protein–protein HADDocking using exclusively pseudocontact shifts

• Journal of Biomolecular NMR
• May 2011

Antimicrobial and Efflux Pump Inhibitory Activity of Caffeoylquinic Acids from Artemisi...

• PLoS ONE
• April 2011

A Multidomain Flexible Docking Approach to Deal with Large Conformational Changes in th...

• Structure
• April 2011

CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking...

• PLoS ONE
• March 2011

Characterizing the N- and C-terminal Small Ubiquitin-like Modifier (SUMO)-interacting M...

• Journal of Biological Chemistry
• March 2011

Structural and Biochemical Characterization of NarE, an Iron-containing ADP-ribosyltran...

• Journal of Biological Chemistry
• March 2011

A structure-based benchmark for protein-protein binding affinity

• Protein Science
• February 2011

Human galectin-3 (Mac-2 antigen): Defining molecular switches of affinity to natural gl...

• Biochimica et Biophysica Acta (BBA) - General Subjects
• February 2011

Adhesion/Growth-Regulatory Galectins: Insights into Their Ligand Selectivity Using Natu...

• January 2011

1H, 13C and 15N assignment of the GNA1946 outer membrane lipoprotein from Neisseria men...

• Biomolecular NMR Assignments
• December 2010

Are Scoring Functions in Protein−Protein Docking Ready to Predict Interactomes? Clues f...

• Journal of Proteome Research
• November 2010

Understanding the Role of the Josephin Domain in the PolyUb Binding and Cleavage Proper...

• PLoS ONE
• August 2010

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

• Biomolecular NMR Assignments
• August 2010

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

• Proteins Structure Function and Bioinformatics
• August 2010

Plectasin, a Fungal Defensin, Targets the Bacterial Cell Wall Precursor Lipid II

• Science
• May 2010

Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s...

• Nucleic Acids Research
• May 2010

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues f...

• Journal of Proteome Research
• May 2010

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

• May 2010

The HADDOCK web server for data-driven biomolecular docking

• Nature Protocols
• April 2010

Building Macromolecular Assemblies by Information-driven Docking

• Molecular & Cellular Proteomics
• March 2010

The eNMR platform for structural biology

• Journal of Structural and Functional Genomics
• March 2010

Structure of the DNA-bound BRCA1 C-terminal Region from Human Replication Factor C p140...

• Journal of Biological Chemistry
• January 2010

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

• BMC Bioinformatics
• January 2010

A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome ...

• Molecular Systems Biology
• October 2009

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

• Nature Methods
• September 2009

A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome ...

• Molecular Systems Biology
• August 2009

Detailed Mechanistic Insights into HIV-1 Sensitivity to Three Generations of Fusion Inh...

• Journal of Biological Chemistry
• July 2009

Specificity and Affinity of Lac Repressor for the Auxiliary Operators O2 and O3 Are Exp...

• Journal of Molecular Biology
• July 2009

3D-DART: a DNA structure modelling server

• Nucleic Acids Research
• May 2009

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

• Proteins Structure Function and Bioinformatics
• March 2009

MINOES: A new approach to select a representative ensemble of structures in NMR studies...

• Proteins Structure Function and Bioinformatics
• March 2009

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

• Proceedings of the National Academy of Sciences
• February 2009

Data-driven homology modelling of P-glycoprotein in the ATP-bound state indicates flexi...

• FEBS Journal
• January 2009

The Prediction of Macromolecular Complexes by Docking

• December 2008

The Vancomycin−Nisin(1−12) Hybrid Restores Activity against Vancomycin Resistant Entero...

• Biochemistry
• December 2008

Hydramacin-1, Structure and Antibacterial Activity of a Protein from the Basal Metazoan...

• Journal of Biological Chemistry
• November 2008

Evolution Rescues Folding of Human Immunodeficiency Virus-1 Envelope Glycoprotein GP120...

• Molecular Biology of the Cell
• November 2008

How Proteins Get in Touch: Interface Prediction in the Study of Biomolecular Complexes

• Current Protein and Peptide Science
• August 2008

A protein-DNA docking benchmark

• Nucleic Acids Research
• June 2008

Deciphering the role of the electrostatic interactions in the α-tropomyosin head-to-tai...

• Proteins Structure Function and Bioinformatics
• June 2008

Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional S...

• January 2008

Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Deter...

• Cell
• November 2007

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

• Proteins Structure Function and Bioinformatics
• September 2007

NMR-based modeling and binding studies of a ternary complex between chicken liver bile ...

• Proteins Structure Function and Bioinformatics
• July 2007

Impaired Peroxisome Proliferator-Activated Receptor γ Function through Mutation of a Co...

• Molecular Endocrinology
• May 2007

Modeling Protein−Protein Complexes Involved in the CytochromecOxidase Copper-Delivery P...

• Journal of Proteome Research
• April 2007

Protein Structures: Relaxation Matrix Refinement

• March 2007

Activity–structure correlations in divergent lectin evolution: fine specificity of chic...

• Glycobiology
• October 2006

Binding Site Structure of One LRP–RAP Complex:Implications for a Common Ligand–Receptor...

• Journal of Molecular Biology
• September 2006

Solvated docking: introducing water into the modelling of biomolecular complexes

• Bioinformatics
• August 2006

Comparative NMR study on the impact of point mutations on protein stability ofPseudomon...

• Protein Science
• August 2006

Two-rung Model of a Left-handed β-Helix for Prions Explains Species Barrier and Strain ...

• Journal of Molecular Biology
• July 2006

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

• Nucleic Acids Research
• June 2006

Intramolecular surface contacts contain information about protein–protein interface reg...

• Bioinformatics
• June 2006

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

• Journal of the American Chemical Society
• June 2006

CORRECTION

• Protein Science
• June 2006

Crystal structure and catalytic mechanism of the LPS 3- <i>O</i> ...

• Proceedings of the National Academy of Sciences
• May 2006

Combining NMR Relaxation with Chemical Shift Perturbation Data to Drive Protein–protein...

• Journal of Biomolecular NMR
• April 2006

Flexible protein–protein docking

• Current Opinion in Structural Biology
• April 2006

Kinetics and Thermodynamics of Type VIII β-Turn Formation: A CD, NMR, and Microsecond E...

• Biophysical Journal
• April 2006

Model for RNA Binding and the Catalytic Site of the RNase Kid of the Bacterial parD Tox...

• Journal of Molecular Biology
• March 2006

WHISCY: What information does surface conservation yield? Application to data-driven do...

• Proteins Structure Function and Bioinformatics
• January 2006

The α-to-β Conformational Transition of Alzheimer's Aβ-(1-42) Peptide in Aqueous Media ...

• ChemBioChem
• January 2006

The Solution Structure of the AppA BLUF Domain: Insight into the Mechanism of Light-Ind...

• ChemBioChem
• December 2005

Describing Partially Unfolded States of Proteins from Sparse NMR Ddata

• Journal of Biomolecular NMR
• November 2005

NMR analysis of protein interactions

• Current Opinion in Chemical Biology
• October 2005

Altered Specificity in DNA Binding by the lac Repressor: A Mutant lac Headpiece that Mi...

• ChemBioChem
• August 2005

Characterization and Structural Analyses of Nonspecific Lipid Transfer Protein 1 from M...

• Biochemistry
• August 2005

Data-driven docking: HADDOCK's adventures in CAPRI

• Proteins Structure Function and Bioinformatics
• June 2005

Various strategies of using residual dipolar couplings in NMR-driven protein docking: A...

• Proteins Structure Function and Bioinformatics
• June 2005

BioMagResBank databases DOCR and FRED containing converted and filtered sets of experim...

• Journal of Biomolecular NMR
• May 2005

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

• Journal of Chemical Theory and Computation
• May 2005

RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restrai...

• Proteins Structure Function and Bioinformatics
• April 2005

Characterization and Structural Analyses of Nonspecific Lipid Transfer Protein 1 from M...

• Biochemistry
• April 2005

The orientations of cytochromecin the highly dynamic complex with cytochromeb5visualize...

• Protein Science
• March 2005

Entropy Calculation of HIV-1 Env gp120, its Receptor CD4, and their Complex: An Analysi...

• Biophysical Journal
• January 2005

Data-driven docking for the study of biomolecular complexes

• FEBS Journal
• December 2004

Solution Structure of the Ubiquitin-conjugating Enzyme UbcH5B

• Journal of Molecular Biology
• November 2004

The nisin–lipid II complex reveals a pyrophosphate cage that provides a blueprint for n...

• Nature Structural & Molecular Biology
• September 2004

NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and it...

• European Journal of Biochemistry
• July 2004

Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes

• Science
• July 2004

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

• Proteins Structure Function and Bioinformatics
• April 2004

DRESS: a database of REfined solution NMR structures

• Proteins Structure Function and Bioinformatics
• April 2004

A Docking Approach to the Study of Copper Trafficking Proteins

• Structure
• April 2004

Structural Model of the UbcH5B/CNOT4 Complex Revealed by Combining NMR, Mutagenesis, an...

• Structure
• April 2004

Insight into Molecular Interactions Between Two PB1 Domains

• Journal of Molecular Biology
• March 2004

On the molecular basis of the recognition of angiotensin II (AII)

• European Journal of Biochemistry
• September 2003

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

• Journal of Magnetic Resonance
• August 2003

Immunogenicity of Peptide-vaccine Candidates Predicted by Molecular Dynamics Simulations

• Journal of Molecular Biology
• May 2003

Molecular Dynamics Studies of a Molecular Switch in the Glucocorticoid Receptor

• Journal of Molecular Biology
• April 2003

HADDOCK:  A Protein−Protein Docking Approach Based on Biochemical or Biophysical Inform...

• Journal of the American Chemical Society
• February 2003

NMR Study of Mersacidin and Lipid II Interaction in Dodecylphosphocholine Micelles

• Journal of Biological Chemistry
• January 2003

Refinement of protein structures in explicit solvent

• Proteins Structure Function and Bioinformatics
• January 2003

• Journal of Biomolecular NMR
• January 2003

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

• The EMBO Journal
• November 2002

Plasticity in protein-DNA recognition: lac repressor interacts with its natural operato...

• The EMBO Journal
• June 2002

Mapping the Targeted Membrane Pore Formation Mechanism by Solution NMR:  The Nisin Z an...

• Biochemistry
• June 2002

The C Terminus of Apocytochromeb562Undergoes Fast Motions and Slow Exchange among Order...

• Biochemistry
• April 2002

Rational design of a subtype-specific peptide vaccine against Neisseria meningitis

• January 2002

• Journal of Biomolecular NMR
• January 2001

Changes in Dynamical Behavior of the Retinoid X Receptor DNA-Binding Domain upon Bindin...

• Biochemistry
• August 2000

Hydration dynamics of the collagen triple helix by NMR11Edited by P. E. Wright

• Journal of Molecular Biology
• July 2000

Sequence-specific HMG box factors recognize 10-12 base pair minor groove motifs

• Journal of Biological Chemistry
• June 2000

The GROMOS96 benchmarks for molecular simulation

• Computer Physics Communications
• June 2000

Localisation and dynamics of sodium counterions around DNA in solution from molecular d...

• European Biophysics Journal
• March 2000

β-hairpin stability and folding: molecular dynamics studies of the first β-hairpin of t...

• Journal of Molecular Biology
• February 2000

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

• Structure
• January 1999

Water molecules in DNA recognition I: hydration lifetimes of trp operator DNA in solu...

• Journal of Molecular Biology
• October 1998

Water molecules in DNA recognition II: a molecular dynamics view of the structure and h...

• Journal of Molecular Biology
• October 1998

Refined Structure oflacRepressor Headpiece (1-56) Determined by Relaxation Matrix Calcu...

• Journal of Molecular Biology
• June 1996

Conformational Variability of Solution Nucelar Magnetic Resonance Structures

• Journal of Molecular Biology
• June 1995

Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by...

• Journal of Molecular Biology
• April 1995

Nuclear Magnetic Resonance Solution Structure of the Arc Repressor Using Relaxation Mat...

• Journal of Molecular Biology
• February 1994

Direct nuclear Overhauser effect refinement of crambin from two-dimensional nmr data us...

• Biopolymers
• January 1994

Time- and ensemble-averaged direct NOE restraints

• Journal of Biomolecular NMR
• January 1994

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

• Annals of the New York Academy of Sciences
• June 1993

“Ensemble” iterative relaxation matrix approach: A new NMR refinement protocol applied ...

• Proteins Structure Function and Bioinformatics
• April 1993

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

• Journal of Biomolecular NMR
• January 1993

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

• Journal of Magnetic Resonance (1969)
• December 1991

Direct NOE refinement of biomolecular structures using 2D NMR data

• Journal of Biomolecular NMR
• September 1991

Toward an NMR R factor

• Journal of Magnetic Resonance (1969)
• February 1991

Effects of strong coupling in multiple-quantum-filtered two-dimensional NOE spectroscopy

• Journal of Magnetic Resonance (1969)
• February 1990