PhD Position in protein protein molecular recognition and design

Academic supervisor:

Universitat Pompeu Fabra and Prof. Gianni De Fabritiis, Icrea research professor, are looking to recruit a young scientist for a PhD of the duration of approximatively 3 years in Barcelona on the topic of protein-protein recognition using molecular simulations.

Aims:

This project aims to develop methods for characterizing molecular recognition between protein-protein and protein-antibodies. The aim is to go substantially beyond the state-of-the-art, exploring new methodologies based on advanced software platforms (www.htmd.org) with the aim to design novel potential therapeutic agents.

We expect the candidate to participate in the development and application of the methods in collaboration with clinical and experimental groups. By working in this project, the researcher will have access to state of the art computational resources using GPUGRID.net and large amount of molecular simulation data. This project is expected to lead to discoveries that will be publishable in the highest impact scientific journals.

Location:

Barcelona, Spain,Barcelona Biomedical Research park. The laboratory is part of the Barcelona Biomedical Research Park which, with a privileged location on the shoreline of the Mediterranean sea, constitutes one of the most exciting interdisciplinary research centres in Southern Europe with more than 1000 scientists in the building alone.

Candidate Profile:

The candidate will preferably have a profile in chemistry, biology, physics or related fields. We seek candidates with a passion for biology and computing, the capability to think out of the box, the ambition to work in very innovative projects and very good communication skills in English. Prior knowledge in molecular simulations, protein-design methods, knowledge-based methods is desirable, but we are really looking for self-motivated, exceptional candidates. Most of the methods will be developped using Python and HTMD. A good knowledge of programming in Python or other programming languages is therefore required.

Facilities:

The candidate will be able to use GPUGRID, one of the largest volunteer computing project worldwide with thousands of GPUs. The laboratory is very well equipped with access to a local GPU and CPU cluster, hundreds of TB of storage and experimental facilities.

The molecular modelling will be using state of the art software environments in molecular modelling and simulations developed by the research group in collaboration with the spin-off company Acellera (www.acellera.com).

There will be ample opportunities to present his/her work at international meetings and conferences and to collaborate with other research groups in USA and Europe.

Funding and Eligibility:

Interested candidates should apply by sending a complete CV and a short letter of presentation indicating their interests together with the names and addresses of three referees to: Gianni De Fabritiis (gianni.defabritiis at upf.edu). The title of this offer must be clearly stated in any communication.

Deadline: To be filled within 2016

Some Relevant References:

  • N. Stanley, S. Esteban and G. De Fabritiis, Kinetic modulation of a disordered protein domain by phosphorylation, Nat. Commun. 5, 5272 (2014).
  • S. Doerr and G. De Fabritiis, On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations, J. Chem. Theory Comput. 10 (5), pp 2064–2069(2014).
  • N Stanley, L Pardo, G De Fabritiis, The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor, in press Scientific Reports (2016).
  • S. Doerr , M.J. Harvey, F. Noé ,G. De Fabritiis, HTMD: High-throughput molecular dynamics for molecular discovery, in press JCTC
  • S. Arena et al., Emergence of multiple EGFR extracellular mutations during cetuximab treatment in colorectal cancer, Clin Cancer Res. 2015 21(9) 2157.