Ph.D. job offer: Improve methods to dock RNA with proteins.
This PhD project focuses on the following aspects:
1. Optimize algorithms for single-stranded RNA docking methodology, based on our previous works
2. Create a RNA-RRM model generation pipeline
3. Incorporate new sources of information for data-driven docking: multiple conformations, low resolution biophysical data, conserved amino-acid – nucleotide contacts
4. Assist with developing a framework of protein design for RRMs
The PhD student will spend few months of secondments at Dynamic Biosensors GmbH (Germany) to relate in silico work to the experimental determination of RNA-RRM binding with biochips, and to learn about commercial software development.
The project is highly interdisciplinary: the day-to-day work involves a lot of programming on atomic representations of proteins and nucleic acids. Good programming skills (preferentially Python and/or C++) are essential. Knowledge of structural biology is very desirable, skills in discrete mathematics and statistics would be appreciated. Most importantly, candidates must be motivated to learn about all disciplines relevant to the project.
Candidates must be fluent either in French or in English.