PhD Position - Study the Protein / Protein Interface Energetics by Means of Free Energy Calculations Performed Using ML/MM Potentials bei Forschungszentrum Jülich

Forschungszentrum Jülich

The department "Computational Molecular Medicine" follows an interdisciplinary and integrative approach, combining INM-9`s theoretical expertise in protein modelling, simulation, free-energy calculations and in silico molecular investigations with practical approaches from the fields of experimental biochemistry and organic synthesis. These physics-based approaches are combined with machine learning methods in order to derive relationships and correlations between molecules on the basis of multi-omic data. Finally, the Computational Molecular Medicine department also contributes to INM-9`s efforts to move to the systemic level. The goal is to relate events at the molecular level to real biological reactions.

Your Job:

Protein–protein interactions (PPIs) mediate a vast number of cellular pathways and processes, making them an important class of targets for drug discovery. However, decades of effort aimed at developing small molecule drugs to modulate PPIs have been rewarded with a relatively modest number of successes. The difficulty is thought to arise primarily from topology; The key issues of code scalability and the time scale problem will be addressed for the first time using a recently developed method that builds on metadynamics - an exact method to compute free energies - and the statistical mechanics of paths.

Expected Results:

Investigation of the protein-protein interface energetic interaction for medically relevant dimers
A ML/MM
Potential model applicable to study protein-protein interfaces

Your Profile:

University degree (Master) in physics, chemistry, applied mathematics or computer science
Experience with UNIX-like operating systems
Mathematical and programming skills (R, Python, Keras,Tensorflow)
Ideal prior knowledge on MD simulations and ML
Excellent knowledge of written and oral English: TOEFL or equivalent evidence of English-speaking skills
Interactive person with good communication skills
Used to work in international teams
Willing to travel in different labs during PhD

Our Offer:

We work on the very latest issues that impact our society and are offering you the chance to actively help in shaping the change! We offer ideal conditions for you to complete your doctoral degree:

A highly motivated working group as well as an international and interdisciplinary working environment at one of Europe’s largest research establishments
Outstanding scientific and technical infrastructure
Opportunity to participate in (international) conferences and project meetings
Continuous scientific mentoring by your scientific advisor
Flexible work (location) arrangements, e.g. remote work
30 days of annual leave and provision for days off between public holidays and weekends (e.g. between Christmas and New Year)
Further development of your personal strengths, e.g. through an extensive range of training courses; a structured program of continuing education and networking opportunities specifically for doctoral researchers via JuDocS, the Jülich Center for Doctoral Researchers and Supervisors: https://www.fz-juelich.de/en/judocsTargeted services for international employees, e.g. through our International Advisory Service

The position is for a fixed term of 3 years. Pay in line with 70 % of pay group 13 of the Collective Agreement for the Public Service (TVöD-Bund) and additionally 60 % of a monthly salary as special payment („Christmas bonus“). Further information on doctoral degrees at Forschungszentrum Jülich including our other locations is available at: https://www.fz-juelich.de/gp/Careers_Docs

We welcome applications from people with diverse backgrounds, e.g. in terms of age, gender, disability, sexual orientation / identity, and social, ethnic and religious origin. A diverse and inclusive working environment with equal opportunities in which everyone can realize their potential is important to us.