Senior Molecular Simulations Scientist

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

Job summary

Flagship Pioneering seeks a Senior/Principal Scientist in Molecular Simulations to lead the physics layer of a drug development AI platform in Cambridge, MA. You will own end-to-end simulation workflows, validate designs before synthesis, and translate results into training signals for generative models.

You will drive MD, enhanced sampling, and free-energy methods, while collaborating with medicinal chemistry and external partners to push portfolios forward.

Qualifications

• PhD in computational chemistry, biophysics, chemical physics, structural biology, or related field; MSc with equivalent industry depth considered.
• 4+ years of post‑PhD molecular simulation experience, at least part in drug discovery (Sr. Scientist); 6+ years with ownership of a method/platform (Principal).
• Deep hands-on MD experience: force fields, parameterization, solvation, equilibration, and failure modes.
• Production experience with at least one enhanced sampling or free energy framework with validation.
• Structure-based drug design fundamentals: docking, pharmacophore, and hot-spot analysis.
• Strong Python, with OpenMM/GROMACS/AMBER/NAMD/Desmond and MD analysis stacks; version control and reproducible workflows.
• Ability to run simulations at scale on GPU/HPC/cloud via automation.

Responsibilities

• Binder characterization: analyze ligand–target complexes across peptides, macrocycles, nanobodies, antibodies.
• Characterize binding sites and cryptic pockets using MD, enhanced sampling, and pocket detection.
• Design validation: triage designs using pose prediction, docking rescoring, and MD stability checks.
• Free energy & affinity: build/validate affinity workflow (FEP/MM-GBSA/PBSA); report accuracy.
• Beyond‑Rule‑of‑5 properties: model conformational behavior and membrane partitioning for macrocycles.
• Simulation‑to‑ML interface: convert simulation outputs into signals for the generative platform.
• Infrastructure & throughput: build reproducible GPU/cloud HPC pipelines; automate setup, QC, analysis at portfolio scale.
• Cross‑functional partnership: work with chemistry, pharmacology, and external biology teams; feed data back to models.

Skills

Python

OpenMM

GROMACS

AMBER/CHARMM/OPLS

NAMD

Desmond

MDAnalysis/MDTraj

RDKit

Version control

Workflow automation

GPU/Cloud

Education

PhD or MSc in related field

Tools

OpenMM

GROMACS

AMBER/CHARMM/OPLS

NAMD

Desmond

MDAnalysis/MDTraj

RDKit

PyMOL/ChimeraX

Job description

Flagship Pioneering seeks a Senior/Principal Scientist in Molecular Simulations to lead the physics layer of a drug development AI platform in Cambridge, MA. You will own end-to-end simulation workflows, validate designs before synthesis, and translate results into training signals for generative models.

You will drive MD, enhanced sampling, and free-energy methods, while collaborating with medicinal chemistry and external partners to push portfolios forward.