Development of Deeprank-GNN - Bonvin Lab, CSB group, UU

Deeprank-GNN is a Graph Neural Network framework to learn interaction patterns from protein-protein interfaces

• See : Deeprank-GNN Github page
• See : Deeprank-GNN documentation

Shape-restrained protein-ligand HADDOCK docking - Bonvin Lab, CSB group, UU

Shape-restrained protein-ligand HADDOCK docking

• See : P.I. Koukos, M.F. Reau and A.M.J.J. Bonvin. Shape-restrained modelling of protein-small molecule complexes with HADDOCK. bioRxiv doi:10.1101/2021.06.10.447890 (2021).

Early versions of this protocol were used to perform drug repurposing on COVID-19 proteins

• See : https://www.bonvinlab.org/covid/

Importance of inactive data in models : application to virtual screening in human health and environnement - example of nuclear receptors - Cnam, GBCM

This section summarizes my PhD work under the supervision of Pr Matthieu Montes.

Study of the evolution of the use of decoy compounds/ true inactive data in CADD benchmarking data sets.

• See : Réau et al, Front. Pharmacol. 2018

Creation of the NR-DBIND (Nuclear Receptors DataBase Including Negative Data)

• See : Réau et al, J. Med. Chem 2019

Identification of computer-aided drug design (CADD) pipelines to identify modulators of different nuclear receptors

• Docking approach
• Pharmacophore modeling approach
• See : Réau et al, Cells 2019

Theranalpha Project (Theranostic TNFa inhibitors) - Cnam, GBCM

The global objective of this project is to design and evaluate in vitro and in vivo theranostic small molecule inhibitors of TNFa to further provide inexpensive anti-TNFa therapies administered orally.

Project coordinator : Pr Marc Port, Laboratoire de Chimie Moléculaire, CNAM
The project is supported by an ANR grant: Read the full ANR project

Collaborators

• Laboratoire CM (Chimie Moléculaire), CNAM, Paris
• Laboratoire GBA (Génomique, Bioinformatique et Applications), CNAM, Paris
• Laboratoire SATIE (Laboratoire des Systèmes et Applications des Technologies de l’Information et de l’Energie)
• PEPTINOV SAS