Computational biology & molecular dynamics modeling

This theme at the interface of mathematics, computer science, physics and biology focuses on modeling and simulation for problems arising from biology.

Enlarge the image
©CB / V. Devillard

Scientific referents

Coordinator: Luba Tchertanov

Scientific leaders:

  • Luba Tchertanov
  • Alain Trouvé
Enlarge the image
Dynamical inter-residue, cross-correlation map, computed for two conformations of KIT shows teh functional dependence of distant regions of KIT ©J. Ledoux, A. Trouvé, L. Tchertanov

Presentation of the thematic area

This research in computational biology or linked to problems in oncology and blood diseases is interdisciplinary at the interface of mathematics, computer science, physics and biology. They focus on the characterization of bio-molecules that are valid and novel therapeutic targets. Researchers study, at the atomistic level, the structural and dynamic properties of biomolecules, represented in the form of 3D numerical models, and search for relationships between their properties and biological function and/or dysfunction leading to serious pathologies.

Research areas developed

  • Modeling/Simulation and Biology/Clinical
  • Modeling/Simulation and Mathematics
  • Receptor Tyrosine Kinases and Cancer
  • Vitamin K Epoxide Reductase and blood coagulation

Key words

3D Modeling; Simulation of the molecular dynamics; Stochastic models; Machine learning; Recognition and affinity; Proteins and complex molecular; Intrinsic disorder and transition; Allosteric regulation; Mutation and cancer; Mutation and blood diseases; Drug resistance; 

Applications

This research has numerous applications mainly in the health field. Such a level of characterization allows us to understand the effects of abnormal molecular processes associated with serious diseases (cancers, blood diseases, inflammatory and neurodegenerative diseases...) and to provide new targets for the development of new molecules (inhibitors/modulators) in order to control these pathophysiological processes.

Key facts

Receptor Tyrosine Kinase KIT

Ledoux J., Trouvé A. & Tchertanov L. The inherent coupling of intrinsically disordered regions in the multidomain receptor tyrosine kinase KIT. Int. J. Mol. Sci. 2022

Receptor Tyrosine Kinase KIT

Ledoux J. & Tchertanov L. Receptor Tyrosine Kinase KIT: A New Look for an Old Receptor. Proceedings of the 9th International Work-Conference on IWBBIO 2020, held in Maspalomas, Gran Canaria, Spain, in June 2022

Order-disorder nature of RTK KIT

Ledoux J. & Tchertanov L. A first comprehensive look at the order-disorder nature of RTK KIT native and carcinogenic targets, Glob J Cancer Ther 8(1): 036-039, 2022.

Invited paper in Kinases Phosphatases 2023

Ledoux, J.; Botnari, M.; Tchertanov, L. Receptor Tyrosine Kinase KIT: Mutation-Induced Conformational Shift Promotes Alternative Allosteric Pockets. Invited paper in Kinases Phosphatases 2023, 1, (4) 220-250.

Vitamin K Epoxide Reductase and blood coagulation

Ledoux J., Stolyarchuk M, Bachelier E., Trouvé A. and Tchertanov L. (2022). Human Vitamin K Epoxide Reductase as a Target of its Redox Protein. Int. J. Mol. Sci. Special Issue: (IDPs) 2.0. 23(7), 3899

Vitamin K Epoxide Reductase and blood coagulation

Ledoux J., Stolyarchuk M. and Tchertanov L. (2022). Human Vitamin K Epoxide Reductase as a Target of its Redox Protein. International Work-Conference on Bioinformatics and Biomedical Engineering. 2022 - 30, 2

Interactions with other themes of the Centre Borelli

Image processing

In this theme, researchers at the Centre Borelli develop mathematical theories and algorithms for processing images and videos.

Simulation and modeling of complex physical systems

The work of this pole concerns the modeling, the mathematical analysis and the simulation of complex physical phenomena.