What if... you could use computational protein design to impact an entire ecosystem of life science companies?

The Role

Pioneering Intelligence (PI) is a Flagship initiative focused on developing and harnessing AI/ML based platforms for innovative applications in life sciences and beyond.  We are seeking a talented Senior Computational Scientist with hands-on experience developing and implementing novel methods and algorithms for computational protein design.  You will be joining a team that is building state-of-the-art biomolecular design platforms powered by the latest AI and computation-based technologies that can accelerate innovation across Flagship’s entire venture ecosystem. 

Responsibilities:

• Work with the PI team to identify, create, implement, benchmark, and scale techniques at the intersection of biophysics and AI for computational protein design oriented towards therapeutic protein modalities including antibodies.
• Work on projects within the Flagship ecosystem to deliver state-of-the-art computational protein design strategies that are tailored to venture’s scientific and business needs.
• Develop, test, deploy and maintain industry quality pipelines on cloud infrastructure.

Qualifications:

• PhD in biochemistry, biophysics, bioinformatics, computational chemistry, computer science, AI/ML, or a related discipline solving biological problems using computational approaches.
• Required: demonstrated experience developing and implementing novel methods and algorithms for computational protein design.
• Demonstrated experience in a programming language such as Python, C/C++, Java, etc.

Preferred:

• 3+ years industry experience.
• Experience with design and modeling software such as Rosetta, RFDiffusion, ProteinMPNN, Chroma, AlphaFold, ESMFold, RoseTTAFold, OSPREY, etc.
• Experience developing novel generative AI, structure, or sequence-based methods for the design of therapeutic proteins.
• Experience training generative AI models for protein design and prediction.
• Experience with bioinformatics approaches for analyzing sequences.
• Experience constructing, annotating, analyzing, and maintaining large databases of protein structures and sequences.
• Experience with modern frameworks for deep learning and machine learning, e.g. PyTorch, JAX, SageMaker, etc.
• Experience with modern software development and cloud services, e.g. Git, Docker, AWS Batch, Step Functions, EKS, etc.

About Flagship

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded 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.

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. 

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please 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.

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.