Mots-Clés

Molecular dynamics simulations Protein conformational ensembles

Description

About the research center

The Inria Centre was established in 1986 and became Centre Inria at Université de Lorraine in 2023. Its growth has been part of the development of the Lorraine site with the University of Lorraine. It also has a branch in Strasbourg, which is developing alongside the University of Strasbourg. The centre has 20 project teams, divided between Nancy, Strasbourg and Saarbrücken. Its activities occupy over 400 people, scientists and research and innovation support staff, including 38 different nationalities.

Context

This research engineer position is part of the project; ANR-JCJC IDPFold, and ANR-PRC VITAL (2025-2029) recently funded by the French National Research Agency (ANR). The engineer will work alongside the memebrs of the research team to study the conformational heterogeneity of proteins, collecting and curating molecular dynamics (MD) simulations data, extracting features, building dataframes for further development, etc.

The position will be supervised by Hamed Khakzad (Junior Professor, Inria). Our team consists of two permanent researchers with several PhD and postdoc members, and is expected to grow by hiring new members. Our main goal is to develop deep learning models, to study, and predict protein structure, interaction, function and to further design synthetic molecules. The team has access to computational resources, including efficient GPUs and CPUs, from different cluster centers including Grid5000, Jean Zay, etc.

Assignment

The selected engineer will collaborate closely with the research team to investigate the conformational heterogeneity of proteins in specific complexes, and in large scale. This role involves running and managing MD simulations to gather high-quality data. The engineer will be responsible for collecting and curating this data, ensuring its accuracy and relevance. They will extract meaningful features from the molecular dynamics simulations, which are crucial for understanding protein dynamics. Additionally, the engineer will compile and refine these features into comprehensive datasets designed for potential future applications. Expertise in data science will be essential for interpreting complex molecular dynamics data and facilitating the development of advanced databases. The engineer will also be expected to stay aware of the latest methodologies in both molecular dynamics simulations to continuously enhance the quality and efficiency of the research outputs.

Main activities

1. Perform and manage molecular dynamics simulations.
2. Collaborate with research team members to study protein conformational heterogeneity.
3. Build and refine databases.
4. Document procedures, results, and insights to support ongoing research efforts.

Skills

• Master or PhD degree in Computer Science, or Bioinformatics
• Proficiency in programming languages (Python) and good coding practices is mandatory*
• Expertise in molecular dynamics simulations.
• Experience in machine learning is a plus
• Ability to work independently and also to work in a team
• Strong analytical and problem-solving skills.
• Excellent oral and written English skills

*applications with no computer science background will not be considered.

Benefits package

• Fully funded position (1+1 years)
• Subsidized meals
• Partial reimbursement of public transport costs
• Professional equipment available (videoconferencing, laptop, etc.)
• Social, cultural and sports events and activities
• Access to vocational training
• Social security coverage

Duration

Duration: 24 months