D-Index & Metrics Best Publications
Alexandre M. J. J. Bonvin

Alexandre M. J. J. Bonvin

Biology and Biochemistry
Netherlands
2023

D-Index & Metrics D-index (Discipline H-index) only includes papers and citation values for an examined discipline in contrast to General H-index which accounts for publications across all disciplines.

Discipline name D-index D-index (Discipline H-index) only includes papers and citation values for an examined discipline in contrast to General H-index which accounts for publications across all disciplines. Citations Publications World Ranking National Ranking
Biology and Biochemistry D-index 79 Citations 25,131 349 World Ranking 2675 National Ranking 63

Research.com Recognitions

Awards & Achievements

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

Overview

What is he best known for?

The fields of study he is best known for:

  • Gene
  • Enzyme
  • DNA

Docking, Computational biology, Searching the conformational space for docking, Stereochemistry and Biochemistry are his primary areas of study. His work in the fields of Docking, such as Macromolecular docking, intersects with other areas such as Haddock. His research integrates issues of Genetics, Experimental data, Protein protein, Molecular Docking Simulation and Data science in his study of Computational biology.

In his research, Algorithm is intimately related to Protein–ligand docking, which falls under the overarching field of Searching the conformational space for docking. His Stereochemistry research incorporates themes from Protein structure, Lantibiotics, Lipid II and Peptide. The various areas that Alexandre M. J. J. Bonvin examines in his Biochemistry study include Antimicrobial, Microbiology and Bacteria.

His most cited work include:

  • HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. (1999 citations)
  • The HADDOCK web server for data-driven biomolecular docking (882 citations)
  • The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. (840 citations)

What are the main themes of his work throughout his whole career to date?

The scientist’s investigation covers issues in Docking, Computational biology, Biochemistry, Protein structure and Crystallography. His research in the fields of Searching the conformational space for docking, Macromolecular docking and Protein protein overlaps with other disciplines such as Haddock. The study incorporates disciplines such as Structural biology and Protein–protein interaction in addition to Computational biology.

His work carried out in the field of Biochemistry brings together such families of science as Biophysics and Stereochemistry. His Protein structure research incorporates elements of Plasma protein binding and Protein folding. His Crystallography study integrates concerns from other disciplines, such as Chemical shift, Nuclear magnetic resonance spectroscopy, Hydrogen bond and Molecular dynamics.

He most often published in these fields:

  • Docking (27.27%)
  • Computational biology (17.01%)
  • Biochemistry (15.25%)

What were the highlights of his more recent work (between 2017-2021)?

  • Docking (27.27%)
  • Computational biology (17.01%)
  • Haddock (8.50%)

In recent papers he was focusing on the following fields of study:

Alexandre M. J. J. Bonvin spends much of his time researching Docking, Computational biology, Haddock, Protein protein and Biological system. His Macromolecular docking study in the realm of Docking interacts with subjects such as Ab initio. His study in Computational biology is interdisciplinary in nature, drawing from both Protein structure, Lipid bilayer, Membrane protein and Function.

Structural biology is closely connected to Membrane associated in his research, which is encompassed under the umbrella topic of Membrane protein. Alexandre M. J. J. Bonvin integrates Haddock and Force field in his studies. His Binding site study deals with Metadynamics intersecting with Small molecule and Druggability.

Between 2017 and 2021, his most popular works were:

  • Assessment of contact predictions in CASP12: co-evolution and deep learning coming of age (114 citations)
  • Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 (40 citations)
  • Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. (32 citations)

In his most recent research, the most cited papers focused on:

  • Gene
  • Enzyme
  • DNA

His scientific interests lie mostly in Docking, Computational biology, Structural biology, Haddock and Biological system. The various areas that Alexandre M. J. J. Bonvin examines in his Docking study include Biophysics and Ligand. The Biophysics study combines topics in areas such as Amino acid, Site-directed mutagenesis and Tetramer.

His Ligand research includes elements of Metadynamics, Molecular dynamics, Molecular recognition, Computational science and Web server. His Computational biology research is multidisciplinary, incorporating elements of Epitope, Antigen, Antibody antigen and Monoclonal antibody. His work deals with themes such as Intermolecular force, van der Waals force, Proteomics and Biochemical engineering, which intersect with Structural biology.

This overview was generated by a machine learning system which analysed the scientist’s body of work. If you have any feedback, you can contact us here.

Best Publications

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

Cyril Dominguez;Rolf Boelens;Alexandre M J J Bonvin.
Journal of the American Chemical Society (2003)

2876 Citations

The HADDOCK web server for data-driven biomolecular docking

Sjoerd J de Vries;Marc van Dijk;Alexandre M J J Bonvin.
Nature Protocols (2010)

1108 Citations

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.
Journal of Molecular Biology (2016)

1029 Citations

Refinement of protein structures in explicit solvent.

Jens P. Linge;Mark A. Williams;Christian A.E.M. Spronk;Alexandre M. J. J. Bonvin.
Proteins (2003)

666 Citations

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

Sjoerd J. de Vries;Aalt D. J. van Dijk;Mickaël Krzeminski;Mark van Dijk.
Proteins (2007)

631 Citations

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.
Nature Structural & Molecular Biology (2004)

592 Citations

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

Charalampos G. Kalodimos;Nikolaos Biris;Alexandre M. J. J. Bonvin;Marc M. Levandoski.
Science (2004)

548 Citations

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.
eLife (2014)

452 Citations

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

Tanja Schneider;Thomas Kruse;Reinhard Wimmer;Imke Wiedemann.
Science (2010)

450 Citations

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.
Cell (2007)

423 Citations

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