Dr. Alexandre M.J.J. Bonvin
Universiteit Utrecht
Professor, Chemistry
Netherlands
My co-authors include
Dr Leon Mario Amzel
M. Natalia D. S. Cordeiro
Professor Yiqun Deng
Find me at
My Publications
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<sub>2P2I</sub>: 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