Fragment-based protein-RNA docking for protein design

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Chauvot de Beauchene
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<div>&nbsp;</div><div>&nbsp;</div><div><strong>Kewords</strong>:&nbsp;protein &ndash; RNA docking, molecular modeling, structural bio-informatics, computational biology, methods development, graph analysis, combinatorics</div><div>&nbsp;</div><div><strong>Context</strong></div><div>&nbsp;</div><div>The PhD project is part of a multi-disciplinary European ITN project called RNAct, involving 8 inter-connected PhD projects in computational and experimental molecular biology, biophysics and system biology. The overarching aim of RNAct is to integrate experiment and computation to design novel RNA-binding proteins, for synthetic biology and bio-analytics. RNAct will create and characterize novel functional RNA-Recognition motifs in proteins, with customized recognition of specific single-stranded RNA (ssRNA).&nbsp;</div><div>See</div><div>&nbsp;</div><div><strong>Project</s… CAPSID team is developing methods to model the 3D structure of biomolecules and their assemblages. Docking consists of modeling a molecular assembly from the 3D structure of each molecule, by sampling the possible relative positions of the two molecules, and evaluating the interaction energy to identify the most stable positioning . We have recently developed a method for modeling protein-bound RNAs by combinatorial assembly of fragments.</div><div>&nbsp;</div><div>The aims of the proposed PhD project are to:</div><div>- Optimize the algorithms for single-stranded RNA docking methodology</div><div>- Specialise the method for a specific RNA-binding domain, the RNA-Recognition Motif (RRM)</div><div>- Automatize a pipeline to generate RRM-protein models&nbsp;</div><div>- Incorporate new sources of information for data-driven docking (multiple protein conformations, biophysical data, conserved amino-acid &ndash; nucleotide contacts)</div><div>- Assist with the development of a framework for RMM design</div><div>&nbsp;</div><div>Read more here:</div><div></div><d… PhD student will spend few months of secondments at Dynamic Biosensors GmbH (Germany) to relate his/her in silico work to the experimental determination of RNA-RRM binding with biochips, and to learn about commercial software development.</div><div><p><strong>Eligibility /&nbsp;</strong><strong>Requirements</strong></p><p>European funding require an&nbsp;international mobility:&nbsp; The candidates must not have resided or carried out their main activity in France for more than 12 months in the 3 years prior to the recruitment.</p><p>Candidates must have a masters degree in any of the relevant disciplines: (bio-)physics, structural biology, bio-informatics or computer science.</p><p>The project is highly interdisciplinary: the day-to-day work involves a lot of programming on atomic representations of proteins and nucleic acids.&nbsp;Good programming skills (preferentially Python and/or C++) are essential. Knowledge of structural biology is very desirable, skills in algorithmic, discrete mathematics and statistics would be appreciated. Most importantly, candidates must be motivated to learn about all disciplines relevant to the project.</p><p>Candidates must be fluent either in French or in English.</p><p>Applications&nbsp;should be sent on the RNAct centralized application web site:; &nbsp;(Select ESR4 project)</p></div><div>&nbsp;</div><br/>
Laboratoire: LORIA (CNRS - INRIA - UL)