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Accueil du site > Jobs - PostDoc - These > A postdoctoral position on methods and algorithms to calculate biomolecular structures in the framework of the Distance Geometry Problem (DGP)

A postdoctoral position on methods and algorithms to calculate biomolecular structures in the framework of the Distance Geometry Problem (DGP)

par Nord & Ile de France - 30 septembre 2020

A postdoctoral position on methods and algorithms to calculate biomolecular structures in the framework of the Distance Geometry Problem (DGP).

A postdoctoral (14 months) position is currently open in the framework of the international ANR project multiBioStruct in collaboration with Taiwan (https://anr.fr/Project-ANR-19-CE45-0019). The project intends to develop novel computational approaches for the exhaustive sampling of disordered protein conformational space by exploiting NMR chemical shift measurements and by employing methods belonging to the DGP class. The project stands on rigid basis given by more than 10 years of previous research activities, which have already confirmed the validity of the approach on a set of small globular protein conformations. Our current aim is to extend its domain of applicability to larger molecules and systems. This extension will require, for example, (i) the developments of Machine Learning (ML) techniques ; (ii) the implementation of novel efficient strategies for global and combinatorial optimization ; and (iii) the development of software tools capable of processing input data from the biochemical labo.

The project’s consortium includes three French teams that have been collaborating on this topic since more than 10 years : IRISA (Rennes), Institut Pasteur (Paris) and Ecole Polytechnique (Palaiseau). Additionally, the project has two international partners (two Academia Sinica’s teams) in Taiwan : one team is now recording NMR measurements on various samples. The two postdoc candidate is expected to actively work in this highly international and highly multi-disciplinary environment, and to interact with all the partners of the consortium.

We seek motivated candidates with a strong background in molecular modeling methods, informatics, with good programming skills in low-level programming languages (C, C++). The candidates need to have a great interest in biological applications.

The postdoc researcher will be recruited at Institut Pasteur, Paris. The position is open from January 2021, for 14 months.

If you’re interested in this position, please don’t hesitate to contact us and to send us your curriculum vitae accompanied with a motivation letter.

Contacts (please send an email to both addresses) :

  • Antonio Mucherino (antonio.mucherino@irisa.fr)
  • Therese Malliavin (therese.malliavin@pasteur.fr)

References

Malliavin TE, Mucherino A, Lavor C, Liberti L. Systematic exploration of protein conformational space using a Distance Geometry approach. J Chem Inf Model 59, 4486-4503 (2019).

Mucherino A, Lin J-H. An efficient exhaustive search for the Discretizable Distance Geometry Problem with interval data. IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS19), Workshop on Computational Optimization (WCO19), Leipzig, Germany, 135-141 (2019).

Worley B, Delhommel F, Cordier F, Malliavin T, Bardiaux B, Wolff N, Nilges M, Lavor C, Liberti L. Tuning interval Branch-and-Prune for protein structure determination. Journal of Global Optimization 72:109-127 (2018).

Liberti L, Lavor C, Maculan N, Mucherino A, Euclidean Distance Geometry and applications. SIAM Review 56:3-69 (2014). Antonio Monari, Ph.D. Ass. Professor