Senior Scientist, Computational Chemistry

What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies to transform health care and sustainability?

At Flagship Labs 107 (FL107), a Flagship Pioneering-backed stealth biotechnology company, we’re pioneering the mastery of protein control: tuning the stability, degradation, and localization, of any protein. By systematically rewriting the rules of protein homeostasis, we’re on a mission to target the “undruggable” and treat the “impossible.” Our innovative approach combines novel biology, medicinal chemistry, and AI/ML-powered molecular design, all driven by our unwavering commitment to dramatically improve patient lives.

Position Summary:We are seeking a highly creative, resourceful, and motivated Senior Scientist to join our Computational chemistry team. The ideal candidate will set up our in-house DNA-encoded library (DEL) data computational and analysis capabilities to support small molecule discovery efforts. Strong candidates will be independent, goal-oriented, and have excellent communication skills. We are seeking individuals who can be highly adaptable and comfortable working in a dynamic and fast-paced collaborative and multidisciplinary environment. This is a unique opportunity to drive the growth of an early-stage biotechnology company where you can meaningfully define the next frontier of protein homeostasis modulators. The successful candidate will play a key role in driving our discovery efforts aimed at developing therapeutic strategies that modulate protein homeostasis.

Key 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.

Qualifications:

• 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.

Preferred Qualifications:

• 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.

What We Offer:

• 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.

Values and Behaviors:

Flagship is an experiment in institutional, entrepreneurial, and innovation practiced in the context of a small company with an insurgent mindset. We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross-functional team environment.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, we encourage you to apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background. The level of the role will be commensurate with the education and years of experience of the identified candidates.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.