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Name: Thibault Tubiana

Type: User

Company: I2BC

Bio: Currently working as a postdoc I2BC institute (https://www.i2bc.paris-saclay.fr) in Stephane Bressanelli's team.

Twitter: ttubiana

Location: Gif-sur-Yvette, France

Blog: http://www.tubiana.me

Thibault Tubiana, PhD.

About me

I am currently a postdoctoral fellow the I2BC institute (Institute for Integrative Biology of the Cell) in the IMAPP Team. I work with moledular modelling and molecular dynamic simulation on viral proteins (Hepatitis E, Hepatitis C, Norovirus) and their interaction with biological membranes.

I was previously at the the University of Bergen in Nathalie Reuter's group working on the depiction of peripheral membrane protein membrane binding site.
I also worked at the Servier research institute (as a postdoctoral fellow) where I developed new methods to increase their bioisosteric molecular 3D fragment knowledge.

During my Ph.D., supervised by Dr. Stephane Bressanelli and Dr. Yves Boulard at the French Atomic Energy Commission (Paris Saclay), I studied the norovirus capsid self-assembly using molecular dynamics, homology modeling, protein/protein docking but also some experiments with S.A.X.S data acquisition and interpretation.

I love Structural bioinformatic, Molecular Modelling, Molecular Dynamics and 3D visualisation.

Github pages:

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

About my work

You can learn more about my work here:

My galery (Checkout my blender gallery): http://tubiana.me/gallery/
My clustering software for molecular dynamic: TTCLust : https://github.com/tubiana/TTClust
My gromacs protocol: https://github.com/tubiana/protocolGromacs
My thesis on Norovirus Capsid Assembly: https://tubiana.me/research/norovirus-capsid-assembly/
All my teaching content on Molecular Mechanic and Molecular Dynamic (Slides and practicals): https://tubiana.me/teaching/kjem220-molecular-modelling/

Contact me

Github Stats

Thibault Tubiana's Projects

alphasub

Submission server for colabfold (alphafold) for I2BC institute

analysismdnotebooks

Personal repository for storing notebooks used for MD Analysis.

colabfold_singularity

Singularity receipe for local colabfold.

colormsawithsse

Generate a image from a multiple sequence alignment (MSA) colored by the secondary structures elements (SSE)

extract_last_frame

Extract last frame from gromacs simulation

fork-molecularnodes

FORK : Addon and nodes for working with structural biology and molecular data in Blender.

gromacsbenchmarkwsl

personal benchmark for Gromacs with WSL.

mdtools

Just a quick repo for small MD tools.

model_analyser

mrccleaner

Correct a MRC file with fftshift and mirror it to have it fully symmetrical and spherical.

msaexplorer

Webinterface for dynamic MSA exploration.

panel-chemistry

🧪📈 🐍. The purpose of the panel-chemistry project is to make it really easy for you to do DATA ANALYSIS and build powerful DATA AND VIZ APPLICATIONS within the domain of Chemistry using using Python and HoloViz Panel.

pbxplore

A suite of tools to explore protein structures with Protein Blocks :snake:

peprmint-web

Web-tool for calculating and visualizing hydrophobic protrusions

propka2graph

This python script take propka output and then do some stat on residues pka.

protocolgromacs

Automatic gromacs protocol from preparation to production with ligand parametrization through

pypdb

A Python API for the RCSB Protein Data Bank (PDB)

rspfilter

Homogeneous filtering of Relion Star Particles File.

screening_protocol

Screening protocol with AUTODOCK-GPU

smdagui_dev

Simple Molecular Dynamic Analysis Graphical interface

ttclust

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)

ttclustgui

Graphical User Interface for TTclust

tubiana

tubiana.github.io

Github page - Tubiana Thibault

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