Engineering Structural Bioinformatics Applications Algorithms And Code Optimization H/F - INRIA

A propos d'Inria

Inria est l'institut national de recherche dédié aux sciences et technologies du numérique. Il emploie 2600 personnes. Ses 215 équipes-projets agiles, en général communes avec des partenaires académiques, impliquent plus de 3900 scientifiques pour relever les défis du numérique, souvent à l'interface d'autres disciplines. L'institut fait appel à de nombreux talents dans plus d'une quarantaine de métiers différents. 900 personnels d'appui à la recherche et à l'innovation contribuent à faire émerger et grandir des projets scientifiques ou entrepreneuriaux qui impactent le monde. Inria travaille avec de nombreuses entreprises et a accompagné la création de plus de 200 start-up. L'institut s'eorce ainsi de répondre aux enjeux de la transformation numérique de la science, de la société et de l'économie.Engineering structural bioinformatics applications : algorithms and code optimization
Le descriptif de l'offre ci-dessous est en Anglais
Type de contrat : CDD

Niveau de diplôme exigé : Bac +5 ou équivalent

Autre diplôme apprécié : PhD

Fonction : Ingénieur scientifique contractuel

A propos du centre ou de la direction fonctionnelle

The Inria centre at Université Côte d'Azur includes 42 research teams and 9 support services. The centre's staff (about 500 people) is made up of scientists of dierent nationalities, engineers, technicians and administrative staff. The teams are mainly located on the university campuses of Sophia Antipolis and Nice as well as Montpellier, in close collaboration with research and higher education laboratories and establishments (Université Côte d'Azur, CNRS, INRAE, INSERM...), but also with the regiona economic players.

With a presence in the fields of computational neuroscience and biology, data science and modeling, software engineering and certification, as well as collaborative robotics, the Inria Centre at Université Côte d'Azur is a major player in terms of scientific excellence through its results and collaborations at both European and international levels.

Contexte et atouts du poste

SCIENTIFIC CONTEXT. Biomolecules, particularly proteins and nucleic acids (DNA and RNA), are essential to biological processes. Their study is typically divided into two main aspects : the structural level, which focuses on their (meta-)stable conformations, and dynamics, which evaluates the stability of these conformations and the rates at which they interconvert. AlphaFold, the program developed by Deepmind, made a very significant step for structural predictions of structured proteins, and its two leaders were co-awarded the 2024 Nobel prize in chemistry. But the question of fast and accurate predictions of dynamical properties remains open. This is a particularly important problem to understand the strength of interactions at the molecular level, with potentially far reaching applications in medicine. The goal of the project EMINENCE-molEcular dynaMics In iNtErNal CoordinatEs, funded by France 2030-see below, is to deliver state-of-the-art modeling tools geared towards biomolecular dynamics, within the Structural Bioinformatics Library.

SOFTWARE : the Structural Bioinformatics Library. The Structural Bioinformatics Library(SBL, https : //sbl.inria.fr) is a comprehensive software environment to model biomolecules, with a unique and versatile design. IT jointly provides (i) low level algorithm classes, (ii) biophysical models, and (iii) applications solving specific problems in structural bioinformatics. Applications are ascribed to two principal categories respectively targeting static and dynamic models, see https://sbl.inria.fr/applications/. To foster genericity, re-usability, efficiency and robustness, the SBL is mainly developed in generic (template based) C++, and consists of 100 C++ packages, 2/3 in the Core, and 1/3 for Applications.

FRANCE 2030. France 2030 is an investment plan aiming at supporting innovative technologies and the ecological transition https://www.economie.gouv.fr/france-2030. The project EMINENCE is supported by the Inria Quadrant Program and receives national funding through The French National Research Agency as part of the France 2030 plan under the reference « ANR24-RRII-0002 », operated by the Inria Quadrant Program. In the framework of France 2030 and the Digital program agency Digital Program Agency - Algorithms, software and usage operated by Inria, the Inria Quadrant Program selected by the General Secretariat for Investment (SGPI) and the Directorate-General for Research and Innovation (DGRI) aims to support scientific risk-taking and to address current and future challenges in research and innovation for and through digital sciences and technology. See https://piq.inria.fr/.

Mission confiée

ENGINEERING POSITION AND TASKS : ALGORITHM ENGINEERING FOR BIOMOLECULAR DYNAMICS.

In modeling biomolecules, internal coordinates in general and torsion angles in particular are much more effective than Cartesian coordinates to generate large amplitude conformational changes. However, using torsion angles is more challenging mathematically, in several respects : necessity to solve inverse problems of the loop closure type, non local effects, sampling biases. We have recently developed several algorithms to explore energy landscapes, and sample loops as well as multiloop systems.

* Main goals/specific tasks
** Optimizing loop and multiloop samplers.
** Optimizing energy landscape explorers.
** Optimizing binding affinity estimators.

Avantages
- Subsidized meals
- Partial reimbursement of public transport costs
- Leave : 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
- Possibility of teleworking (after 6 months of employment) and flexible organization of working hours
- Professional equipment available (videoconferencing, loan of computer equipment, etc.)
- Social, cultural and sports events and activities
- Access to vocational training
- Social security coverage

Rémunération

From 2692 € gross monthly (according to degree and experience)