Postdoctoral Researcher - Biomolecular AI & Protein-Ligand / Protein-Membrane Interaction Modeling

Location: Berlin, Germany; 3 days per week in-office

Company

Microsoft Research AI for Science develops machine learning and artificial intelligence methods for molecular simulation and the discovery of materials, drugs, and chemical reactions.

What you will do

• Design, execute, and analyze large-scale molecular dynamics simulations for protein-ligand and protein-membrane interactions, including free energy perturbation studies.
• Create high-quality, machine learning-ready datasets from scalable data generation campaigns, with defined quality standards and evaluation metrics.
• Build reproducible computational workflows and automation pipelines using Python and distributed computing infrastructure.
• Collaborate with machine learning researchers, computational biologists, and research engineers to integrate simulation outputs into advanced modeling workflows.
• Design model-informed experimentation strategies and validate computational findings against reference calculations and experimental data.
• Lead research projects from ambiguous scientific questions to impactful methods, publications, datasets, software, and research directions.

Requirements

• PhD or equivalent experience in Computational Biology, Structural Biology, Biophysics, Physics, Statistical Mechanics, or a related field.
• Expertise in biomolecular simulation, including system setup, force-field selection, parameterization, and related methodologies.
• Deep theoretical and practical experience with free energy perturbation, alchemical free energy methods, convergence, uncertainty, and simulation quality assessment.
• Experience developing scientific software and computational workflows in Python.
• Ability to lead research projects independently and collaborate across multidisciplinary teams.

Nice to have

• Experience with membrane modeling, including lipid composition selection, equilibration, and simulation setup.
• Experience integrating structural biology or molecular simulation data with machine learning approaches.
• Experience generating, curating, or managing large-scale scientific datasets.
• Experience collaborating with machine learning researchers on data generation or model development.

Culture & Benefits

• Resident Researcher contract for 2 years.
• Highly collaborative, cross-disciplinary research environment.
• Opportunity to contribute to biomedical research, drug discovery, publications, datasets, and open-source software.