Senior Molecular Simulations Scientist for AI‑Driven Design

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

Benefits offered by this job

Equal opportunity employer

Job summary

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

You will characterize how binders engage targets and validate generated designs before synthesis, operating at the interface of structure-based modeling and generative ML. You will run MD, enhanced sampling, FEP/MM-GBSA, and develop reproducible pipelines on GPU cloud or HPC, collaborating with medicinal chemistry and external partners.

Qualifications

• PhD or MSc with industry depth in computational chemistry, biophysics, or structural biology.
• 4+ years post‑PhD molecular simulation experience; 6+ years with ownership of a method or platform.

Responsibilities

• Characterize binder engagement and validate designs via MD, docking, and free energy methods.
• Develop and own affinity prediction workflows (FEP/MM-GBSA/PMSA).
• Build scalable simulation pipelines on GPU cloud or HPC.

Skills

Python

OpenMM

GROMACS

MDAnalysis/MDTraj

RDKit

GPU/Cloud automation

Education

PhD in computational chemistry/biophysics/structural biology

Tools

AMBER/CHARMM/OPLS/GAFF/OpenFF

GROMACS

NAMD

Desmond

MDAnalysis

RDKit

Job description

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

You will characterize how binders engage targets and validate generated designs before synthesis, operating at the interface of structure-based modeling and generative ML. You will run MD, enhanced sampling, FEP/MM-GBSA, and develop reproducible pipelines on GPU cloud or HPC, collaborating with medicinal chemistry and external partners.