Senior Scientist, Computational Chemistry

Flagship Pioneering - Cambridge, MA

Full-time - Senior

Cambridge, MA

Professional, Scientific, and Technical Services

About the position

The Senior Scientist in Computational Chemistry at Flagship Labs 107 will play a pivotal role in establishing the computational and analytical capabilities for DNA-encoded library (DEL) data to support small molecule discovery. This position requires a highly creative and motivated individual who can thrive in a dynamic, collaborative environment, driving the growth of an early-stage biotechnology company focused on protein homeostasis modulation.

Responsibilities

• Serve as inaugural member of the Computational chemistry team, establishing core infrastructure and workflows.
• Lead, design and execute processes for DEL data integration, including DEL compound management and metadata capture of experiments.
• Drive development and implementation of new computational tools and methodologies (e.g., machine learning models, data exploration, visualization) to strengthen DEL data analysis.
• Serve as a key contributor with experimental teams to drive design of robust DEL experiments (e.g., designs, controls, library compositions).
• Analyze and interpret data from computational experiments, and provide insights and recommendations to guide decision-making.
• Manage relationships with vendors, CROs, and consultants for external workflows and input.
• Present findings to the team, provide strategic input on project direction, while ensuring rapid turnaround of analysis to drive achievement of key project goals.
• Act as a thought leader for advancements in the field of computational chemistry, applying this knowledge to new and ongoing projects.

Requirements

• Ph.D. in Computational Chemistry, Medicinal Chemistry, Biochemistry, or a related discipline and 5+ years of professional experience preferably with small molecule drug discovery or preclinical development industry experience, or master's degree and 6+ years of industry experience.
• Extensive knowledge and experience in the design and implementation of computational and engineering solutions applied to high throughput screening. Experience with DNA-encoded library screening is a plus.
• Proficiency in Python and familiarity with python packages (e.g., Scikit-learn, Pandas, NumPy, and equivalent tools) for data science.
• Experience in data mining, database management and design, statistical analysis of large data sets.
• Experience in PyTorch or equivalent tools.
• Experience integrating with ELN and LIMS systems, adhering to robust data capture practices and ensuring team compliance.
• Excellent communication and presentation skills, with the ability to convey complex scientific concepts to both technical and non-technical audiences.
• Strong analytical skills with the ability to interpret complex datasets and derive meaningful insights.
• Proven ability to work effectively in a collaborative team environment and manage multiple projects simultaneously.
• Resourceful problem solver and self-starter.

Nice-to-haves

• Experience in computational chemistry drug design and optimization approaches including ligand-based and structure-based (Autodock, rDock, or similar).
• Experience with AWS or similar.
• Experience in protein degradation and/or the development of protein degraders or other heterobifunctional molecules.
• Prior industry experience.

Benefits

• Opportunity to lay the scientific foundation of a transformative platform company as an early employee, and to serve as a key contributor to the development of new technologies in the protein degradation field.
• Custom-tailored role to maximize impactful contributions, professional growth, and scientific interests.
• Weekly lunches, monthly social events, and community lunchroom with free snacks, cold brew coffee tap, and a vibrant community with scientists and entrepreneurs.
• A collaborative and inclusive work environment that values diversity and innovation.
• Access to state-of-the-art facilities and cutting-edge technologies.