Senior Scientist, Computational Protein Design

About Abiologics

Abiologics is a Flagship Pioneering company developing Synteins™ — a transformative class of fully synthetic proteins composed entirely of artificial building blocks such as D-amino acids and non-canonical residues. SynteinsTM are designed to transcend the limitations of traditional biologics, with improved oral stability, immune evasion, and metabolic durability — all while being fully programmable by design.

Powered by a proprietary AI-enabled discovery platform, Abiologics integrates generative design, automated synthesis, and rapid experimental screening to enable iterative optimization at scale.

Position Summary

We are seeking a Protein Design Scientist to join the Computational Protein Design team and help drive structure-based design and optimization of synthetic proteins. This is a highly interdisciplinary role at the interface of computational design, structural biology, and protein engineering.

Ideal candidates have deep experience in de novo protein design, miniproteins, and binders engineering and are eager to push the boundaries of non-natural protein design in a fast-moving, data-rich environment.

Key Responsibilities

• Design and execute SynteinsTM engineering campaigns to generate drug candidates.

• Create computational design strategies to deliver drug candidates drawing from array of ML tools and Rosetta scripts.

• Collaborate with computation, chemistry, and experimental biology teams to optimize designs for function, solubility, and stability.

• Integrate structural and biophysical data (e.g., binding, CD, HDX-MS, CryoEM) into iterative optimization cycles

Qualifications

Required

• PhD in structural biology, biophysics, protein design, or related field

• 2+ years of hands-on experience in structure-guided protein design

• Demonstrated proficiency with modern structure prediction and design tools such as RFdiffusion, proteinMPNN, AF2, Boltz2, BoltzGen, Rosetta or equivalent SOTA tools for in-silico protein engineering.

• Strong understanding of the biophysics of protein folding and interface energetics

• Demonstrated ability to progress designs from concept to experimental testing

• Excellent communication skills

Preferred

• Experience designing minibinders or proteins <100 AAs

• Familiarity with non-canonical amino acid design

• Familiarity with molecular dynamics tools.

• Exposure to high-throughput or automated protein engineering environments

• Prior work on platform-based or early-stage biotech teams

Why Join Abiologics

• Help invent a new class of programmable synthetic proteins

• Be part of a high-velocity discovery platform with real-time synthesis and screening

• Collaborate with a deeply interdisciplinary, mission-driven team

• Redefine the limits of what proteins can do

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

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.

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The salary range for this role is $146,000 - $209,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Abiologics, Inc currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Abiologics, Inc's good faith estimate as of the date of publication and may be modified in the future.