I am currently a CNRS Researcher (CRCN) at the I2BC Institute (Institute for Integrative Biology of the Cell), in the IMAPP Team. My research focuses on molecular modeling and molecular dynamics simulations of viral proteins (Hepatitis E, Hepatitis C, Norovirus) and their interactions with themselves, human proteins and biological membranes (working a lot with AlphaFold2, AlphaFold3 and derivates).

Previously, I worked in Nathalie Reuter’s group at the University of Bergen, where I studied the membrane-binding sites of peripheral membrane proteins.
I also held a postdoctoral position at the Servier Research Institute, developing new methods to expand their 3D bioisosteric fragment library.

During my Ph.D., under the supervision of Dr. Stéphane Bressanelli and Dr. Yves Boulard at the French Atomic Energy Commission (CEA, Paris-Saclay), I investigated Norovirus capsid self-assembly using molecular dynamics, homology modeling, protein-protein docking, and SAXS data acquisition and interpretation.

I am passionate about structural bioinformatics, molecular modeling, molecular dynamics, and 3D visualization.

• Alfafold3 and Boltz2 json/yaml generator
  Generate Alphafold3 (for local use) and boltz2 yaml file interactivelly
  https://tubiana.github.io/afbuilderjson/

• MD Steps Calculator
  Calculate the number of MD steps from the timestep and total simulation time.
  https://tubiana.github.io/mdstepscalculator/

• UniProt ID to Sequence
  Converts a list of UniProt IDs into one-line formatted sequences compatible with the AF3 server.
  https://tubiana.github.io/uniprot_to_seq/

• AlphaFold 3 Analysis
  Drop your AlphaFold 3 archive to visualize all five PAE matrices, pLDDT scores, and models.
  https://tubiana.github.io/af3_analysis/

Learn more about my work here:

• Blender Gallery
  A showcase of molecular renderings and 3D visualizations.
  http://tubiana.me/gallery/

• TTClust
  A clustering tool for molecular dynamics simulations.
  https://github.com/tubiana/TTClust

• GROMACS Protocol
  My personal GROMACS workflow and best practices.
  https://github.com/tubiana/protocolGromacs

• PhD Thesis
  Research on Norovirus capsid assembly.
  https://tubiana.me/research/norovirus-capsid-assembly/

• Teaching Materials
  Course content for Molecular Mechanics and Molecular Dynamics (slides + practicals).
  https://tubiana.me/teaching/kjem220-molecular-modelling/

Feel free to reach out:
thibault [dot] tubiana [at] i2bc [dot] paris-saclay [dot] fr