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

    Article • Communications Biology, January 2024, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  2. DeepRank-GNN-esm: a graph neural network for scoring protein–protein models using protein language model

    Article • Bioinformatics Advances, January 2024, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  3. Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

  4. Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

    Article • Proteins Structure Function and Bioinformatics, October 2023, Wiley

    Dr. Alexandre M.J.J. Bonvin

  5. An antibiotic from an uncultured bacterium binds to an immutable target

    Article • Cell, September 2023, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  6. A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance

    Article • Life Science Alliance, August 2023, Life Science Alliance, LLC

    Dr. Alexandre M.J.J. Bonvin

  7. ARCTIC-3D: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

    Article • July 2023, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

  8. Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

    Article • July 2023, Authorea, Inc.

    Dr. Alexandre M.J.J. Bonvin

  9. Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

    Article • PROTEOMICS, June 2023, Wiley

    Dr. Alexandre M.J.J. Bonvin

  10. DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

  11. Improving the quality of co‐evolution intermolecular contact prediction with DisVis

    Article • Proteins Structure Function and Bioinformatics, May 2023, Wiley

    Dr. Alexandre M.J.J. Bonvin

  12. A new antibiotic from an uncultured bacterium binds to an immutable target

    Article • May 2023, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

  13. MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein–Protein Docking Conformations

    Article • Biomolecules, January 2023, MDPI AG

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Bioinformatics, November 2022, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  15. PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation

    Article • Nature Communications, November 2022, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  16. Information-Driven Antibody–Antigen Modelling with HADDOCK

    Article • November 2022, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • November 2022, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nature, August 2022, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  19. Pathogen-sugar interactions revealed by universal saturation transfer analysis

    Article • Science, July 2022, American Association for the Advancement of Science

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Chemical Theory and Computation, June 2022, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  21. Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine

    Article • Frontiers in Molecular Biosciences, March 2022, Frontiers

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, February 2022, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Structure, February 2022, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

  25. No dance, no partner! A tale of receptor flexibility in docking and virtual screening

    Article • January 2022, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • December 2021, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nature Communications, December 2021, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nature Communications, October 2021, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  29. Information-driven modeling of biomolecular complexes

    Article • Current Opinion in Structural Biology, October 2021, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, September 2021, Wiley

    Dr. Alexandre M.J.J. Bonvin

  31. Shape-Restrained Modeling of Protein–Small-Molecule Complexes with High Ambiguity Driven DOCKing

    Article • Journal of Chemical Information and Modeling, August 2021, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Chemical Theory and Computation, August 2021, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  33. Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

    Article • Frontiers in Molecular Biosciences, July 2021, Frontiers

    Dr. Alexandre M.J.J. Bonvin

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

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

  35. 50 years of PDB: a catalyst in structural biology

    Article • Nature Methods, May 2021, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Magnetic Resonance, April 2021, Copernicus GmbH

    Dr. Alexandre M.J.J. Bonvin

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

    Article • April 2021, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

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

    Article • February 2021, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

  39. Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN

    Article • Nucleic Acids Research, February 2021, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  40. MENSAdb: a thorough structural analysis of membrane protein dimers

    Article • Database, January 2021, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  41. Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

    Article • Processes, December 2020, MDPI AG

    Dr. Alexandre M.J.J. Bonvin

  42. Integrative modeling of membrane-associated protein assemblies

    Article • Nature Communications, December 2020, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  43. Author Correction: Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides

    Article • Communications Chemistry, November 2020, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  44. Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides

    Article • Communications Chemistry, November 2020, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, November 2020, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Structure, October 2020, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  47. Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations

    Article • Frontiers in Molecular Biosciences, August 2020, Frontiers

    Dr. Alexandre M.J.J. Bonvin

  48. Integrative Modeling of Membrane-associated Protein Assemblies

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nature Microbiology, July 2020, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Bioinformatics, July 2020, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  51. Mode of action of teixobactins in cellular membranes

    Article • Nature Communications, June 2020, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • F1000Research, April 2020, Faculty of 1000, Ltd.

    Dr. Alexandre M.J.J. Bonvin, Dr Anastassis Perrakis, rik wierenga, Dr Bohdan Schneider, Dr John M Hancock

  53. Biological vs. Crystallographic Protein Interfaces: An Overview of Computational Approaches for Their Classification

    Article • Crystals, February 2020, MDPI AG

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, January 2020, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Chemical Science, January 2020, Royal Society of Chemistry

    Dr. Alexandre M.J.J. Bonvin

  56. Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and Computations

    Article • BIO-PROTOCOL, January 2020, Bio-Protocol, LLC

    Dr. Alexandre M.J.J. Bonvin

  57. Coarse-grained (hybrid) integrative modeling of biomolecular interactions

    Article • Computational and Structural Biotechnology Journal, January 2020, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  58. iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines

    Article • SoftwareX, January 2020, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  59. Protein–Protein Modeling Using Cryo-EM Restraints

    Article • January 2020, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  60. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

    Article • Structure, December 2019, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Computer-Aided Molecular Design, November 2019, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  62. Modeling Antibody-Antigen Complexes by Information-Driven Docking

    Article • Structure, November 2019, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  63. Integrative modelling of biomolecular complexes

    Article • Journal of Molecular Biology, November 2019, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, October 2019, Wiley

    Dr. Alexandre M.J.J. Bonvin

  65. Computational approaches to therapeutic antibody design: established methods and emerging trends

    Article • Briefings in Bioinformatics, October 2019, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  66. Sharing Data from Molecular Simulations

    Article • Journal of Chemical Information and Modeling, October 2019, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Chemical Theory and Computation, October 2019, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  68. MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing

    Article • Frontiers in Molecular Biosciences, October 2019, Frontiers

    Dr. Alexandre M.J.J. Bonvin

  69. iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines

    Article • September 2019, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, August 2019, Wiley

    Dr. Alexandre M.J.J. Bonvin

  71. Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems

    Article • Proteins Structure Function and Bioinformatics, August 2019, Wiley

    Dr. Alexandre M.J.J. Bonvin

  72. LightDock goes information-driven

    Article • Bioinformatics, August 2019, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • July 2019, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

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

    Article • ACS Chemical Biology, June 2019, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Bioinformatics, June 2019, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Bioinformatics, May 2019, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  77. LightDock goes information-driven

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Chemical Information and Modeling, March 2019, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  79. Natural helix 9 mutants of PPARγ differently affect its transcriptional activity

    Article • Molecular Metabolism, February 2019, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  80. Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein-protein interactions ready for it?

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, January 2019, Wiley

    Dr. Alexandre M.J.J. Bonvin

  81. West-Life: A Virtual Research Environment for structural biology

    Article • Journal of Structural Biology X, January 2019, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  82. Information-Driven Modelling of Antibody-Antigen Complexes

    Article • SSRN Electronic Journal, January 2019, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • F1000Research, December 2018, Faculty of 1000, Ltd.

    Mikael trellet, Dr. Alexandre M.J.J. Bonvin

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

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

  85. pdb-tools: a swiss army knife for molecular structures

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, December 2018, Wiley

    Dr. Alexandre M.J.J. Bonvin

  87. A Membrane Protein Complex Docking Benchmark

    Article • Journal of Molecular Biology, December 2018, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • BMC Bioinformatics, November 2018, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  89. An enhanced-sampling MD-based protocol for molecular docking

    Article • October 2018, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

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

    Article • International Journal of Molecular Sciences, September 2018, MDPI AG

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Bioinformatics, September 2018, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Computer-Aided Molecular Design, August 2018, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Grid Computing, August 2018, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  94. Defining distance restraints in HADDOCK

    Article • Nature Protocols, June 2018, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • May 2018, Cold Spring Harbor Laboratory Press

    Dr. Alexandre M.J.J. Bonvin

  96. Computational Tools for the Structural Characterization of Proteins and Their Complexes from Sequence-Evolutionary Data

    Article • March 2018, Wiley

    Dr. Alexandre M.J.J. Bonvin

  97. Using big-data to understand the protein interface landscape

    Article • December 2017, MDPI AG

    Dr. Alexandre M.J.J. Bonvin

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

    Article • November 2017, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, November 2017, Wiley

    Dr. Alexandre M.J.J. Bonvin

  100. Membrane proteins structures: A review on computational modeling tools

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

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Computer-Aided Molecular Design, August 2017, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Scientific Reports, August 2017, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nature Methods, August 2017, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Angewandte Chemie International Edition, August 2017, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, July 2017, Wiley

    Dr. Alexandre M.J.J. Bonvin

  106. Abstracts

    Article • European Biophysics Journal, June 2017, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • The Journal of Immunology, April 2017, The American Association of Immunologists

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Molecular Biology, February 2017, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  109. Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK

    Article • January 2017, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  110. Prediction of Biomolecular Complexes

    Article • January 2017, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • BIO-PROTOCOL, January 2017, Bio-Protocol, LLC

    Dr. Alexandre M.J.J. Bonvin

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

    Article • The Journal of Immunology, November 2016, The American Association of Immunologists

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, November 2016, Wiley

    Dr. Alexandre M.J.J. Bonvin

  114. A benchmark testing ground for integrating homology modeling and protein docking

    Article • Proteins Structure Function and Bioinformatics, November 2016, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nature Communications, November 2016, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  116. Structure of the bacterial plant-ferredoxin receptor FusA

    Article • Nature Communications, October 2016, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Frontiers in Molecular Biosciences, August 2016, Frontiers

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Bioinformatics, August 2016, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Structural Biology, August 2016, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • International Journal of Molecular Sciences, July 2016, MDPI AG

    Dr. Alexandre M.J.J. Bonvin, M. Natalia D. S. Cordeiro

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

    Article • Protein Engineering Design and Selection, June 2016, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, June 2016, Wiley

    Daisuke Kihara, Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Biological Chemistry, May 2016, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Briefings in Bioinformatics, March 2016, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  125. Data publication with the structural biology data grid supports live analysis

    Article • Nature Communications, March 2016, Nature

    Rachelle Gaudet, Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Molecular Biology, February 2016, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  127. The solution structure of the kallikrein-related peptidases inhibitor SPINK6

    Article • Biochemical and Biophysical Research Communications, February 2016, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Biochemistry and Molecular Biology Education, January 2016, Wiley

    Dr. Alexandre M.J.J. Bonvin

  129. 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

    Article • Journal of Chemical Information and Modeling, December 2015, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • International Journal of Molecular Sciences, December 2015, MDPI AG

    Dr. Alexandre M.J.J. Bonvin

  131. Editorial overview: Protein–protein interactions

    Article • Current Opinion in Structural Biology, December 2015, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • FEBS Letters, October 2015, Wiley

    Dr. Alexandre M.J.J. Bonvin

  133. Structure-Function Relationships of Antimicrobial Peptides and Proteins with Respect to Contact Molecules on Pathogen Surfaces

    Article • Current Topics in Medicinal Chemistry, September 2015, Bentham Science Publishers

    Dr Mushira Abdulaziz Enani, Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Molecular Biology, September 2015, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of the American Chemical Society, August 2015, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • eLife, July 2015, eLife

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Structure, July 2015, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Structure, July 2015, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Frontiers in Genetics, June 2015, Frontiers

    Dr Fotis E. Psomopoulos, Mr Rafael C Jimenez, Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of the American Chemical Society, June 2015, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • June 2015, Faculty of 1000, Ltd.

    Dr. Alexandre M.J.J. Bonvin

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

    Article • June 2015, Faculty of 1000, Ltd.

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nature Structural & Molecular Biology, June 2015, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin, Professor Michele Vendruscolo, Professor Diana R. Tomchick

  144. DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes: Fig. 1.

    Article • Bioinformatics, May 2015, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nature Methods, May 2015, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Biomolecular NMR, May 2015, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Structure, May 2015, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, January 2015, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • AIMS Biophysics, January 2015, American Institute of Mathematical Sciences (AIMS)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • PLoS Pathogens, December 2014, PLOS

    Dr. Alexandre M.J.J. Bonvin

  151. Information-Driven Modeling of Protein-Peptide Complexes

    Article • December 2014, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  152. Binding Hotspots of BAZ2B Bromodomain: Histone Interaction Revealed by Solution NMR Driven Docking

    Article • Biochemistry, October 2014, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  153. Mass Spec Studio for Integrative Structural Biology

    Article • Structure, October 2014, Elsevier

    Linda Wordeman, Dr. Alexandre M.J.J. Bonvin

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

    Article • eLife, September 2014, eLife

    Dr. Alexandre M.J.J. Bonvin

  155. NMR-Based Modeling and Refinement of Protein 3D Structures

    Article • September 2014, Springer Science + Business Media

    Professor Geerten W. Vuister, Dr. Alexandre M.J.J. Bonvin

  156. Information-Driven Structural Modelling of Protein–Protein Interactions

    Article • September 2014, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Molecular Biology, July 2014, Elsevier

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

  158. Information-driven modeling of large macromolecular assemblies using NMR data

    Article • Journal of Magnetic Resonance, April 2014, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  159. Integrative computational modeling of protein interactions

    Article • FEBS Journal, March 2014, Wiley

    Dr. Alexandre M.J.J. Bonvin

  160. HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein–Protein Interaction Inhibitors

    Article • Journal of Chemical Information and Modeling, February 2014, American Chemical Society (ACS)

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

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

    Article • Proceedings of the National Academy of Sciences, January 2014, Proceedings of the National Academy of Sciences

    Dr. Alexandre M.J.J. Bonvin

  162. Modeling Protein–Protein Complexes Using the HADDOCK Webserver “Modeling Protein Complexes with HADDOCK”

    Article • January 2014, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  163. Ion Channel - Ion Channel Interaction at Atomic Resolution

    Article • Biophysical Journal, January 2014, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  164. A Single Inter-Domain Salt Bridge within the Human Argonaute 2 Protein Crucially Affects Protein Folding and Consequently Enzymatic Activity

    Article • Biophysical Journal, January 2014, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  165. Molecular origins of binding affinity: seeking the Archimedean point

    Article • Current Opinion in Structural Biology, December 2013, Elsevier

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

  166. Protein–protein interactions

    Article • Current Opinion in Structural Biology, December 2013, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  167. Blind prediction of interfacial water positions in CAPRI

    Article • Proteins Structure Function and Bioinformatics, November 2013, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • PLoS Pathogens, November 2013, PLOS

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, October 2013, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, October 2013, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, August 2013, Wiley

    Dr. Alexandre M.J.J. Bonvin

  172. Improving 3D structure prediction from chemical shift data

    Article • Journal of Biomolecular NMR, August 2013, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proceedings of the National Academy of Sciences, July 2013, Proceedings of the National Academy of Sciences

    Dr. Alexandre M.J.J. Bonvin

  174. Unveiling the Interaction of Vanadium Compounds with Human Serum Albumin by Using1H STD NMR and Computational Docking Studies

    Article • European Journal of Inorganic Chemistry, July 2013, Wiley

    Dr. Alexandre M.J.J. Bonvin

  175. Solvated protein–DNA docking using HADDOCK

    Article • Journal of Biomolecular NMR, April 2013, Springer Science + Business Media

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

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

    Article • Acta Crystallographica Section D Biological Crystallography, April 2013, International Union of Crystallography

    Dr. Alexandre M.J.J. Bonvin

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

    Article • PLoS ONE, March 2013, PLOS

    Dr. Alexandre M.J.J. Bonvin

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

    Article • PLoS Pathogens, March 2013, PLOS

    Dr. Alexandre M.J.J. Bonvin

  179. Structural Determinants of Specific Lipid Binding to Potassium Channels

    Article • Journal of the American Chemical Society, March 2013, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  180. Advances in integrative modeling of biomolecular complexes

    Article • Methods, March 2013, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  181. Short-Chain Fatty Acids Stimulate Angiopoietin-Like 4 Synthesis in Human Colon Adenocarcinoma Cells by Activating Peroxisome Proliferator-Activated Receptor  

    Article • Molecular and Cellular Biology, January 2013, ASM Journals

    Dr. Alexandre M.J.J. Bonvin

  182. HADDOCK

    Article • January 2013, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  183. Gentamicin Binds to the Megalin Receptor as a Competitive Inhibitor Using the Common Ligand Binding Motif of Complement Type Repeats

    Article • Journal of Biological Chemistry, December 2012, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr. Alexandre M.J.J. Bonvin

  184. Solvated protein–protein docking using Kyte‐Doolittle‐based water preferences

    Article • Proteins Structure Function and Bioinformatics, December 2012, Wiley

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of The Royal Society Interface, December 2012, Royal Society Publishing

    Dr. Alexandre M.J.J. Bonvin

  186. WeNMR: Structural Biology on the Grid

    Article • Journal of Grid Computing, November 2012, Springer Science + Business Media

    Professor Geerten W. Vuister, Dr. Alexandre M.J.J. Bonvin

  187. Rapid prediction of multi-dimensional NMR data sets

    Article • Journal of Biomolecular NMR, November 2012, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  188. Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network

    Article • PLoS Computational Biology, November 2012, PLOS

    Dr. Alexandre M.J.J. Bonvin

  189. In support of the BMRB

    Article • Nature Structural & Molecular Biology, September 2012, Springer Science + Business Media

    Dr Patrick C A van der Wel, Dr. Alexandre M.J.J. Bonvin, Professor Michele Vendruscolo

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

    Article • Biophysical Journal, July 2012, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Chemical Theory and Computation, June 2012, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  192. Clustering biomolecular complexes by residue contacts similarity

    Article • Proteins Structure Function and Bioinformatics, May 2012, Wiley

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Chemical Theory and Computation, April 2012, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  194. Protein–Protein Docking with HADDOCK

    Article • March 2012, Wiley

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

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

    Article • Structure, February 2012, Elsevier

    Professor Michele Vendruscolo, Professor Geerten W. Vuister, Dr. Alexandre M.J.J. Bonvin

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

    Article • BMC Structural Biology, January 2012, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  197. Antimicrobial activity of carbon nanotubes.

    Article • January 2012, CABI Publishing

    Dr. Alexandre M.J.J. Bonvin

  198. Explicit Treatment of Water Molecules in Data-Driven Protein–Protein Docking: The Solvated HADDOCKing Approach

    Article • November 2011, Springer Science + Business Media

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Molecular Biology, November 2011, Elsevier

    Professor Yaoqi Zhou, Dr. Alexandre M.J.J. Bonvin

  200. Next challenges in protein–protein docking: from proteome to interactome and beyond

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, September 2011, Wiley

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

  201. Quantitative use of chemical shifts for the modeling of protein complexes

    Article • Proteins Structure Function and Bioinformatics, July 2011, Wiley

    Dr. Alexandre M.J.J. Bonvin

  202. Protein–protein HADDocking using exclusively pseudocontact shifts

    Article • Journal of Biomolecular NMR, May 2011, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  203. Antimicrobial and Efflux Pump Inhibitory Activity of Caffeoylquinic Acids from Artemisia absinthium against Gram-Positive Pathogenic Bacteria

    Article • PLoS ONE, April 2011, PLOS

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin, Prof Michael R Hamblin

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

    Article • Structure, April 2011, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • PLoS ONE, March 2011, PLOS

    Dr. Alexandre M.J.J. Bonvin

  206. Characterizing the N- and C-terminal Small Ubiquitin-like Modifier (SUMO)-interacting Motifs of the Scaffold Protein DAXX

    Article • Journal of Biological Chemistry, March 2011, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr. Alexandre M.J.J. Bonvin

  207. Structural and Biochemical Characterization of NarE, an Iron-containing ADP-ribosyltransferase fromNeisseria meningitidis

    Article • Journal of Biological Chemistry, March 2011, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr. Alexandre M.J.J. Bonvin

  208. A structure‐based benchmark for protein–protein binding affinity

    Article • Protein Science, February 2011, Wiley

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

  209. Human galectin-3 (Mac-2 antigen): Defining molecular switches of affinity to natural glycoproteins, structural and dynamic aspects of glycan binding by flexible ligand docking and putative regulatory sequences in the proximal promoter region

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

    Dr. Alexandre M.J.J. Bonvin

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

    Article • January 2011, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  211. 1H, 13C and 15N assignment of the GNA1946 outer membrane lipoprotein from Neisseria meningitidis

    Article • Biomolecular NMR Assignments, December 2010, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  212. Are Scoring Functions in Protein−Protein Docking Ready to Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

    Article • Journal of Proteome Research, November 2010, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  213. Understanding the Role of the Josephin Domain in the PolyUb Binding and Cleavage Properties of Ataxin-3

    Article • PLoS ONE, August 2010, PLOS

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Biomolecular NMR Assignments, August 2010, Springer Science + Business Media

    Dr Marco Soriani, Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, July 2010, Wiley

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

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

    Article • Science, May 2010, American Association for the Advancement of Science

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nucleic Acids Research, May 2010, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • May 2010, World Scientific Pub Co Pte Lt

    Dr. Alexandre M.J.J. Bonvin

  219. The HADDOCK web server for data-driven biomolecular docking

    Article • Nature Protocols, April 2010, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  220. Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

    Article • Journal of Proteome Research, April 2010, American Chemical Society (ACS)

    Dr Panagiotis L Kastritis, Dr. Alexandre M.J.J. Bonvin

  221. Building Macromolecular Assemblies by Information-driven Docking

    Article • Molecular & Cellular Proteomics, March 2010, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr. Alexandre M.J.J. Bonvin

  222. The eNMR platform for structural biology

    Article • Journal of Structural and Functional Genomics, March 2010, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Biological Chemistry, January 2010, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • BMC Bioinformatics, January 2010, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Molecular Systems Biology, October 2009, EMBO

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nature Methods, September 2009, Nature

    Professor Geerten W. Vuister, Dr. Alexandre M.J.J. Bonvin

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

    Article • Molecular Systems Biology, August 2009, EMBO

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Biological Chemistry, July 2009, American Society for Biochemistry & Molecular Biology (ASBMB)

    Professor Yiqun Deng, Dr. Alexandre M.J.J. Bonvin

  229. Specificity and Affinity of Lac Repressor for the Auxiliary Operators O2 and O3 Are Explained by the Structures of Their Protein–DNA Complexes

    Article • Journal of Molecular Biology, July 2009, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  230. 3D-DART: a DNA structure modelling server

    Article • Nucleic Acids Research, May 2009, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, March 2009, Wiley

    Dr Anastassis Perrakis, Dr. Alexandre M.J.J. Bonvin

  232. MINOES: A new approach to select a representative ensemble of structures in NMR studies of (partially) unfolded states. Application to Δ25-PYP

    Article • Proteins Structure Function and Bioinformatics, March 2009, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proceedings of the National Academy of Sciences, February 2009, Proceedings of the National Academy of Sciences

    Dr. Alexandre M.J.J. Bonvin

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

    Article • FEBS Journal, January 2009, Wiley

    Dr. Alexandre M.J.J. Bonvin

  235. The Prediction of Macromolecular Complexes by Docking

    Article • December 2008, Wiley

    Dr. Alexandre M.J.J. Bonvin

  236. The Vancomycin−Nisin(1−12) Hybrid Restores Activity against Vancomycin Resistant Enterococci†

    Article • Biochemistry, December 2008, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Biological Chemistry, November 2008, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr. Alexandre M.J.J. Bonvin

  238. Evolution Rescues Folding of Human Immunodeficiency Virus-1 Envelope Glycoprotein GP120 Lacking a Conserved Disulfide Bond

    Article • Molecular Biology of the Cell, November 2008, American Society for Cell Biology (ASCB)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Current Protein and Peptide Science, August 2008, Bentham Science Publishers

    Dr. Alexandre M.J.J. Bonvin

  240. A protein-DNA docking benchmark

    Article • Nucleic Acids Research, June 2008, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  241. Deciphering the role of the electrostatic interactions in the α-tropomyosin head-to-tail complex

    Article • Proteins Structure Function and Bioinformatics, June 2008, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • January 2008, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Cell, November 2007, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, September 2007, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, July 2007, Wiley

    Dr. Alexandre M.J.J. Bonvin

  246. Impaired Peroxisome Proliferator-Activated Receptor γ Function through Mutation of a Conserved Salt Bridge (R425C) in Familial Partial Lipodystrophy

    Article • Molecular Endocrinology, May 2007, Endocrine Society

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Proteome Research, April 2007, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  248. Protein Structures: Relaxation Matrix Refinement

    Article • March 2007, Wiley

    Dr. Alexandre M.J.J. Bonvin

  249. Activity–structure correlations in divergent lectin evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16

    Article • Glycobiology, October 2006, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Molecular Biology, September 2006, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Bioinformatics, August 2006, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  252. Comparative NMR study on the impact of point mutations on protein stability ofPseudomonas mendocinalipase

    Article • Protein Science, August 2006, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Molecular Biology, July 2006, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Nucleic Acids Research, June 2006, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

  255. Intramolecular surface contacts contain information about protein–protein interface regions

    Article • Bioinformatics, June 2006, Oxford University Press (OUP)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of the American Chemical Society, June 2006, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  257. CORRECTION

    Article • Protein Science, June 2006, Wiley

    Dr. Alexandre M.J.J. Bonvin

  258. Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL fromPseudomonas aeruginosa

    Article • Proceedings of the National Academy of Sciences, May 2006, Proceedings of the National Academy of Sciences

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Biomolecular NMR, April 2006, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  260. Flexible protein–protein docking

    Article • Current Opinion in Structural Biology, April 2006, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  261. Kinetics and Thermodynamics of Type VIII β-Turn Formation: A CD, NMR, and Microsecond Explicit Molecular Dynamics Study of the GDNP Tetrapeptide

    Article • Biophysical Journal, April 2006, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  262. Model for RNA Binding and the Catalytic Site of the RNase Kid of the Bacterial parD Toxin–Antitoxin System

    Article • Journal of Molecular Biology, March 2006, Elsevier

    Maria Chiara Monti, Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, January 2006, Wiley

    Dr. Alexandre M.J.J. Bonvin

  264. The α-to-β Conformational Transition of Alzheimer's Aβ-(1-42) Peptide in Aqueous Media is Reversible: A Step by Step Conformational Analysis Suggests the Location of β Conformation Seeding

    Article • ChemBioChem, January 2006, Wiley

    Dr. Alexandre M.J.J. Bonvin

  265. The Solution Structure of the AppA BLUF Domain: Insight into the Mechanism of Light-Induced Signaling

    Article • ChemBioChem, December 2005, Wiley

    Dr. Alexandre M.J.J. Bonvin

  266. Describing Partially Unfolded States of Proteins from Sparse NMR Ddata

    Article • Journal of Biomolecular NMR, November 2005, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  267. NMR analysis of protein interactions

    Article • Current Opinion in Chemical Biology, October 2005, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  268. Altered Specificity in DNA Binding by the lac Repressor: A Mutant lac Headpiece that Mimics the gal Repressor

    Article • ChemBioChem, August 2005, Wiley

    Dr. Alexandre M.J.J. Bonvin

  269. Characterization and Structural Analyses of Nonspecific Lipid Transfer Protein 1 from Mung Bean

    Article • Biochemistry, August 2005, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  270. Data-driven docking: HADDOCK's adventures in CAPRI

    Article • Proteins Structure Function and Bioinformatics, June 2005, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, June 2005, Wiley

    Dr. Alexandre M.J.J. Bonvin

  272. BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures

    Article • Journal of Biomolecular NMR, May 2005, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Chemical Theory and Computation, May 2005, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  274. RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

    Article • Proteins Structure Function and Bioinformatics, April 2005, Wiley

    Dr. Alexandre M.J.J. Bonvin

  275. Characterization and Structural Analyses of Nonspecific Lipid Transfer Protein 1 from Mung Bean†,‡

    Article • Biochemistry, April 2005, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  276. The orientations of cytochromecin the highly dynamic complex with cytochromeb5visualized by NMR and docking using HADDOCK

    Article • Protein Science, March 2005, Wiley

    Dr. Alexandre M.J.J. Bonvin

  277. Entropy Calculation of HIV-1 Env gp120, its Receptor CD4, and their Complex: An Analysis of Configurational Entropy Changes upon Complexation

    Article • Biophysical Journal, January 2005, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  278. Data-driven docking for the study of biomolecular complexes

    Article • FEBS Journal, December 2004, Wiley

    Dr. Alexandre M.J.J. Bonvin

  279. Solution Structure of the Ubiquitin-conjugating Enzyme UbcH5B

    Article • Journal of Molecular Biology, November 2004, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  280. The nisin–lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics

    Article • Nature Structural & Molecular Biology, September 2004, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  281. NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist

    Article • European Journal of Biochemistry, July 2004, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Science, July 2004, American Association for the Advancement of Science

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Proteins Structure Function and Bioinformatics, April 2004, Wiley

    Dr. Alexandre M.J.J. Bonvin

  284. DRESS: a database of REfined solution NMR structures

    Article • Proteins Structure Function and Bioinformatics, April 2004, Wiley

    Professor Geerten W. Vuister, Dr. Alexandre M.J.J. Bonvin

  285. A Docking Approach to the Study of Copper Trafficking Proteins

    Article • Structure, April 2004, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  286. Structural Model of the UbcH5B/CNOT4 Complex Revealed by Combining NMR, Mutagenesis, and Docking Approaches

    Article • Structure, April 2004, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  287. Insight into Molecular Interactions Between Two PB1 Domains

    Article • Journal of Molecular Biology, March 2004, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • European Journal of Biochemistry, September 2003, Wiley

    Dr Leon Mario Amzel, Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Magnetic Resonance, August 2003, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  290. Immunogenicity of Peptide-vaccine Candidates Predicted by Molecular Dynamics Simulations

    Article • Journal of Molecular Biology, May 2003, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  291. Molecular Dynamics Studies of a Molecular Switch in the Glucocorticoid Receptor

    Article • Journal of Molecular Biology, April 2003, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of the American Chemical Society, February 2003, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  293. NMR Study of Mersacidin and Lipid II Interaction in Dodecylphosphocholine Micelles

    Article • Journal of Biological Chemistry, January 2003, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr. Alexandre M.J.J. Bonvin

  294. Refinement of protein structures in explicit solvent

    Article • Proteins Structure Function and Bioinformatics, January 2003, Wiley

    Dr. Alexandre M.J.J. Bonvin

  295. Article • Journal of Biomolecular NMR, January 2003, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • The EMBO Journal, November 2002, Wiley

    Dr. Alexandre M.J.J. Bonvin

  297. Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator O1 through alternative conformations of its DNA-binding domain

    Article • The EMBO Journal, June 2002, Wiley

    Dr. Alexandre M.J.J. Bonvin

  298. Mapping the Targeted Membrane Pore Formation Mechanism by Solution NMR:  The Nisin Z and Lipid II Interaction in SDS Micelles

    Article • Biochemistry, June 2002, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

  299. The C Terminus of Apocytochromeb562Undergoes Fast Motions and Slow Exchange among Ordered Conformations Resembling the Folded State†

    Article • Biochemistry, April 2002, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • January 2002, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  301. Article • Journal of Biomolecular NMR, January 2001, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  302. Changes in Dynamical Behavior of the Retinoid X Receptor DNA-Binding Domain upon Binding to a 14 Base-Pair DNA Half Site†

    Article • Biochemistry, August 2000, American Chemical Society (ACS)

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Molecular Biology, July 2000, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Biological Chemistry, June 2000, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr. Alexandre M.J.J. Bonvin

  305. The GROMOS96 benchmarks for molecular simulation

    Article • Computer Physics Communications, June 2000, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • European Biophysics Journal, March 2000, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  307. β-hairpin stability and folding: molecular dynamics studies of the first β-hairpin of tendamistat 1 1Edited by A. R. Fersht

    Article • Journal of Molecular Biology, February 2000, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Structure, January 1999, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  309. Water molecules in DNA recognition I: hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy 1 1Edited by B. Honig

    Article • Journal of Molecular Biology, October 1998, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Molecular Biology, October 1998, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  311. Refined Structure oflacRepressor Headpiece (1-56) Determined by Relaxation Matrix Calculations from 2D and 3D NOE Data: Change of Tertiary Structure upon Binding to thelacOperator

    Article • Journal of Molecular Biology, June 1996, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  312. Conformational Variability of Solution Nucelar Magnetic Resonance Structures

    Article • Journal of Molecular Biology, June 1995, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Molecular Biology, April 1995, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  314. Nuclear Magnetic Resonance Solution Structure of the Arc Repressor Using Relaxation Matrix Calculations

    Article • Journal of Molecular Biology, February 1994, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  315. Direct nuclear Overhauser effect refinement of crambin from two-dimensional nmr data using a slow-cooling annealing protocol

    Article • Biopolymers, January 1994, Wiley

    Dr. Alexandre M.J.J. Bonvin

  316. Time- and ensemble-averaged direct NOE restraints

    Article • Journal of Biomolecular NMR, January 1994, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Annals of the New York Academy of Sciences, June 1993, Wiley

    Dr. Alexandre M.J.J. Bonvin

  318. “Ensemble” iterative relaxation matrix approach: A new NMR refinement protocol applied to the solution structure of crambin

    Article • Proteins Structure Function and Bioinformatics, April 1993, Wiley

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Biomolecular NMR, January 1993, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Magnetic Resonance (1969), December 1991, Elsevier

    Dr. Alexandre M.J.J. Bonvin

  321. Direct NOE refinement of biomolecular structures using 2D NMR data

    Article • Journal of Biomolecular NMR, September 1991, Springer Science + Business Media

    Dr. Alexandre M.J.J. Bonvin

  322. Toward an NMR R factor

    Article • Journal of Magnetic Resonance (1969), February 1991, Elsevier

    Dr. Alexandre M.J.J. Bonvin

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

    Article • Journal of Magnetic Resonance (1969), February 1990, Elsevier

    Dr. Alexandre M.J.J. Bonvin