Senior Scientist II, Protein Design Generation

About Generate:Biomedicines

Generate:Biomedicines is a new kind of therapeutics company – existing at the intersection of machine learning, biological engineering, and medicine – pioneering Generative Biology™ to create breakthrough medicines where novel therapeutics are computationally generated, instead of being discovered. The Company has built a machine learning-powered biomedicines platform with the potential to generate new drugs across a wide range of biologic modalities. This platform represents a potentially fundamental shift in what is possible in the field of biotherapeutic development.

We pursue this audacious vision because we believe in the unique and revolutionary power of generative biology to radically transform the lives of billions, with an outsized opportunity for patients in need. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us!

Generate:Biomedicines was founded in 2018 by Flagship Pioneering and has received nearly $700 million in funding, providing the resources to rapidly scale the organization. The Company has offices in Somerville and Andover, Massachusetts with 300+ employees.

The Role: 

Generate:Biomedicines is seeking a highly skilled and motivated Senior Scientist II to join the Computational Protein Generation (CPG) team. This role requires deep expertise in computational protein design with hands-on experience successfully applying modern protein design and structure prediction tools. The ideal candidate will have a strong track record of integrating protein dynamics and experimental structure data into practical protein design workflows, advancing innovative therapeutic molecules. 

You will collaborate closely with Machine Learning, Protein Sciences, and Preclinical Discovery and Development groups, participating directly in a rigorous and iterative design-build-test-learn cycle. Your work will be pivotal in shaping cutting-edge protein design methodologies and contributing meaningfully to therapeutic discovery. 

Here's how you will contribute:

• Lead the development, validation, and optimization of computational protein generation and design algorithms, integrating protein dynamics and structural data. 

• Collaborate closely with cross-functional teams to define design criteria and deliver optimized proteins aligned with therapeutic program goals. 

• Apply state-of-the-art protein design, structure prediction, and analysis tools practically and effectively in real-world therapeutic scenarios. 

• Analyze computational outputs alongside experimental data to iteratively refine methodologies and validate design approaches. 

• Communicate and present research findings clearly, fostering productive discussions in multidisciplinary project settings. 

• Mentor junior team members, providing expertise and guidance in computational methods and protein biophysics. 

The Ideal Candidate will have:

• PhD in Computational Biology, Biophysics, Bioinformatics, or a related discipline. 

• 6+ years of relevant industry experience focused on computational protein design, ideally in therapeutic contexts. 

• Proven practical expertise in applying modern protein design and protein structure prediction tools  

• Deep expertise in modeling protein dynamics, and demonstrated success in integrating protein dynamics and experimental structure data into protein design workflows. 

• Strong understanding of protein structure-function relationships, biophysical characterization, and computational analysis. 

• Excellent cross-disciplinary communication and collaboration skills, including experience interacting with experimental biologists and computational scientists. 

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Generate:Biomedicines is 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: Generate:Biomedicines does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Generate:Biomedicines or its employees is strictly prohibited unless contacted directly by the Company’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Generate:Biomedicines and the Company will not owe any referral or other fees with respect thereto.