Lead Molecular Simulations Scientist for Drug Discovery AI

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 146,000 - 237,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Job summary

Flagship Pioneering, Inc. in Cambridge, MA, seeks a Sr. Scientist/Principal Scientist for Molecular Simulations to build the physics layer of a drug design AI platform.

You will own end‑to‑end simulation workflows that connect structure-based modeling with generative ML, turning outputs into training signals for the platform. You will lead ligand–target characterization, binding-pocket assessment, and validation of generated designs before synthesis, with extensive use of MD, free energy

Qualifications

• PhD or MSc with strong research in computational chemistry or related field.
• Post-PhD molecular simulation experience in drug discovery is preferred.
• Experience running MD simulations at scale on GPUs or HPC.

Responsibilities

• Characterize ligand–target complexes using structural and dynamic analysis.
• Assess binding pockets with MD, enhanced sampling, and pocket detection.

Skills

Molecular dynamics

Python

OpenMM

GROMACS

NAMD

MDAnalysis

MDTraj

Education

PhD in computational chemistry/biophysics

MSc with industry depth considered

Tools

AMBER/CHARMM/OPLS

GAFF/OpenFF

solvation & ions

Job description

Flagship Pioneering, Inc. in Cambridge, MA, seeks a Sr. Scientist/Principal Scientist for Molecular Simulations to build the physics layer of a drug design AI platform.

You will own end‑to‑end simulation workflows that connect structure-based modeling with generative ML, turning outputs into training signals for the platform. You will lead ligand–target characterization, binding-pocket assessment, and validation of generated designs before synthesis, with extensive use of MD, free energy