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Alexandre M. J. J. Bonvin

Alexandre M. J. J. Bonvin

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Biology and Biochemistry
Netherlands
2023

D-Index & Metrics

Biology and Biochemistry

D-Index
91
Citations
36708
World Ranking
2288
National Ranking
55

Research.com Recognitions

  • 2023 - Research.com Biology and Biochemistry in Netherlands Leader Award

Overview

Alexandre M. J. J. Bonvin is affiliated with Utrecht University in the Netherlands. Their research primarily focuses on the field of Biochemistry, Genetics, and Molecular Biology, with a significant number of publications in molecular biology as a subfield. Their scientific contributions span areas such as computational theory and mathematics, materials chemistry, radiology, nuclear medicine and imaging, and ecology.

Bonvin's work covers several key topics within molecular sciences, including:

  • Protein Structure and Dynamics
  • Computational Drug Discovery Methods
  • Enzyme Structure and Function
  • RNA and Protein Synthesis Mechanisms
  • Monoclonal and Polyclonal Antibodies Research
  • Bioinformatics and Genomic Networks
  • Microbial Metabolic Engineering and Bioproduction

Their recent publications demonstrate a strong focus on structural biology, computational modeling, and molecular simulations. Notable papers include:

  • Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem, 2021, Florence Research (University of Florence)
  • Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development, 2020, Processes
  • The HADDOCK2.4 web server for integrative modeling of biomolecular complexes, 2024, Nature Protocols
  • Teixobactin kills bacteria by a two-pronged attack on the cell envelope, 2022, Nature
  • DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces, 2022, Bioinformatics

Frequent collaborators in Bonvin's research include Panagiotis I. Koukos, Rodrigo V. Honorato, Brian Jiménez-García, Marco Giulini, and Manon Réau. These coauthors have contributed to a substantial number of joint publications, indicating active and ongoing collaborative research efforts.

The scientist's work appears regularly in several publication venues, with the most frequent outlets being:

  • Zenodo (CERN European Organization for Nuclear Research)
  • bioRxiv (Cold Spring Harbor Laboratory)
  • Proteins Structure Function and Bioinformatics
  • Nature Communications
  • Journal of Chemical Information and Modeling

Best Publications

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

    Cyril Dominguez;Rolf Boelens;Alexandre M J J Bonvin

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

    G.C.P. van Zundert;J.P.G.L.M. Rodrigues;M. Trellet;C. Schmitz

  • The HADDOCK web server for data-driven biomolecular docking

    Sjoerd J de Vries;Marc van Dijk;Alexandre M J J Bonvin

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

    Li Xue;João Garcia Lopes Maia Rodrigues;Panagiotis L Kastritis;Alexandre Mjj Bonvin

  • Refinement of protein structures in explicit solvent.

    Jens P. Linge;Mark A. Williams;Christian A.E.M. Spronk;Alexandre M. J. J. Bonvin

  • The Nisin-Lipid II Complex Reveals a Pyrophosphate Cage that Provides a Blueprint for Novel Antibiotics

    Shang-Te D Hsu;Eefjan Breukink;Eugene Tischenko;Mandy A G Lutters

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

    Charalampos G. Kalodimos;Nikolaos Biris;Alexandre M. J. J. Bonvin;Marc M. Levandoski

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

    Tanja Schneider;Thomas Kruse;Reinhard Wimmer;Imke Wiedemann

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

    Thomas A Hopf;Charlotta P I Schärfe;Charlotta P I Schärfe;João P G L M Rodrigues;Anna G Green

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

    Anna Vangone;Alexandre M J J Bonvin

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

    Panagiotis L. Kastritis;Alexandre M. J. J. Bonvin

  • Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

    Rodrigo Vargas Honorato;Panagiotis I. Koukos;Brian Jiménez-García;Andrei Tsaregorodtsev

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

    Thom Vreven;Iain H. Moal;Anna Vangone;Brian G. Pierce

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

    Ioannis Gelis;Alexandre M.J.J. Bonvin;Dimitra Keramisanou;Marina Koukaki

  • 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

    Simona Tomaselli;Veronica Esposito;Paolo Vangone;Nico A. J. van Nuland;Nico A. J. van Nuland

  • Flexible protein-protein docking.

    Alexandre M. J. J. Bonvin

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

    Aart J. Nederveen;Jurgen F. Doreleijers;Wim Vranken;Zachary Miller

  • 3D-DART: a DNA structure modelling server

    Marc van Dijk;Alexandre M. J. J. Bonvin

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

    Sjoerd J. de Vries;Alexandre M. J. J. Bonvin

  • Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

    Outi M. H. Salo-Ahen;Ida Alanko;Rajendra Bhadane;Alexandre M. J. J. Bonvin

Frequent Co-Authors

Rolf Boelens
Rolf Boelens Utrecht University
Robert Kaptein
Robert Kaptein Utrecht University
Marc Baldus
Marc Baldus Utrecht University
Eefjan Breukink
Eefjan Breukink Utrecht University
Wim F. Vranken
Wim F. Vranken Vrije Universiteit Brussel
Zhiping Weng
Zhiping Weng University of Massachusetts Chan Medical School
Geerten W. Vuister
Geerten W. Vuister University of Leicester
Paul A. Bates
Paul A. Bates The Francis Crick Institute
Juan Fernández-Recio
Juan Fernández-Recio Spanish National Research Council
Shoshana J. Wodak
Shoshana J. Wodak Vrije Universiteit Brussel

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