Research Associate, Computational Ion Channel Design, Synthetic and Structural Biology

The Institute of Molecular and Clinical Ophthalmology Basel (IOB) seeks a highly motivated Research Associate. IOB is a research institute combining basic and clinical research. Its mission is to drive innovations in understanding vision and its diseases and develop new therapies for vision loss. It is a place where your expertise will be valued, your abilities challenged and your knowledge expanded.

We are recruiting a Research Associate in computational ion channel and membrane‑protein design (protein design structural and synthetic biology). In this role you will drive an end‑to‑end design‑build‑test cycle:
computationally design engineered ion channels (e.g. light‑responsive membrane proteins),
translate designs into expression constructs and validate function in mammalian systems in collaboration with colleagues performing quantitative assays (with access to high‑throughput electrophysiology and advanced imaging). The position combines modern structure‑based and generative design approaches with hands‑on experimental execution (mammalian cell culture, transfection/transduction, expression optimisation and protein/function characterization).

• Own the computational and structural design cycle for ion channels and light‑sensitive membrane proteins (concept design, hypotheses in silico, screening and selection of candidates for testing) in close interaction with experimental and translational collaborators.
• Define clear design objectives and success criteria and translate designs into practical construct and assay plans.
• Develop and apply learned‑model‑assisted protein design workflows (structure prediction, inverse folding/sequence design, sequence scoring and generative proposal methods) and integrate them with experimental feedback across iterative design cycles.
• Execute a targeted experimental validation workflow (limited hands‑on bench work): routine mammalian cell culture, DNA cloning/construct handling as needed, transfection/transduction and small‑scale expression testing in HEK/CHO (or equivalent).
• Coordinate and interpret functional readouts generated with the team (e.g. electrophysiology, imaging, biochemical assays) using results to iterate designs.
• Communicate progress and results clearly in internal updates, written documentation and project meetings; contribute to conference presentations and manuscripts as appropriate.
• Maintain accurate records and effective day‑to‑day communication with your supervisor and collaborators.

• PhD (or equivalent experience) in computational biology, protein engineering, structural biology, biophysics, biochemistry, molecular/cell biology or a closely related field.
• 3 years of post‑graduate (or equivalent) experience with at least two of the following:
  • computational/structure‑based protein design (especially membrane proteins or ion channels)
  • learned‑model‑assisted protein design workflows (e.g. structure prediction, inverse folding/sequence design, protein language‑model–based sequence scoring and generative sequence/structure proposal tools)
  • generative or library‑based design and screening strategies (incl. directed evolution)
  • molecular biology for rapid design‑build‑test cycles (cloning, construct design, expression optimisation)
  • metagenomic mining/discovery pipelines and annotation
  • quantitative functional screening (microplate assays and/or electrophysiology/imaging readouts)
• Strong motivation to develop and refine methods primarily in silico with a light but competent experimental component.
• Highly organised and precise; comfortable managing multiple design iterations with rigorous documentation and version control.
• Solid programming and data‑analysis skills (e.g. Python) and experience working with structural biology and protein‑design software/tool chains (e.g. Rosetta, structure‑prediction workflows such as Alpha Fold–derived or equivalent, inverse‑folding/sequence‑design and generative design tools, MD/analysis tool chains).
• Practical competence with mammalian cell culture and sterile technique; familiarity with BSL‑1/BSL‑2 environments.
• Evidence of impact in protein design (e.g. first‑author work, open‑source contributions,…