# Senior / Principal Scientist, Molecular Simulations at Flagship Pioneering

- Company: Flagship Pioneering
- What the company does: Pioneering Partnerships Latest News.
- Company website: https://www.flagshippioneering.com
- Type: VC firms
- Level: Principal and up
- Location: Cambridge, MA USA
- Work setup: On-site
- Pay: $146K to $237K base salary per year (USD)
- Posted: 2026-10-01
- Apply by: 2026-11-15
- Apply: https://boards.greenhouse.io/flagshippioneeringinc/jobs/8843622002?gh_jid=8843622002&utm_source=1752vc&utm_medium=careers
- Page: https://www.1752.vc/careers/jobs/flagship-pioneering-senior-principal-scientist-molecular-simulations/

## About the role

FL117 , a venture-backed stealth AI x bio company, is seeking a Sr. Scientist / Principal Scientist, Molecular Simulations . Here you will build the physics layer of a drug development AI platform. You will characterize how binders engage their targets and validate generated designs before they are committed to synthesis. You will work at the interface of structure-based modeling and generative ML, turning simulation output into training signals. Found on 1752vc Careers, the job board for startup and VC roles.

## What they're looking for

- PhD in computational chemistry, biophysics, chemical physics, structural biology, or a related field, MSc with equivalent industry depth considered
- 4+ years of post-PhD molecular simulation experience, at least part of it in a drug discovery setting (Sr. Scientist), 6+ years with demonstrated ownership of a method or platform (Principal)
- Structure-based drug design fundamentals: docking and pose evaluation, pharmacophore and hot-spot analysis, and critical assessment of experimental and predicted structures
- Strong Python, with fluency in simulation toolchains (OpenMM, GROMACS, AMBER, NAMD, or Desmond) and analysis stacks (MDAnalysis/MDTraj, RDKit), version control and reproducible workflows as habit, not aspiration
- Demonstrated ability to run simulations at scale on GPU, HPC, or cloud infrastructure through automation rather than manual per-system setup
- Judgment about method cost versus decision value: able to say when a multi-week free energy campaign is warranted and when docking plus a short MD run is enough

Tags: Research/Discovery

Source: 1752vc Careers, https://www.1752.vc/careers/jobs/flagship-pioneering-senior-principal-scientist-molecular-simulations/