Sr. Scientist, Generative Protein Design

Job Description

Our company Discovery Biologics Disruptive Technologies is seeking an exceptional AI/ML protein engineer to drive the application of structure-based computational protein design and optimization methods to support our biotherapeutic portfolio. The individual is expected to partner closely with cross-functional discovery programs to turn great ideas into valuable medicines that help patients. The role is based out of our Cambridge, MA facility.  

We are on a quest for cures and are committed to be the world’s premier, most research-intensive biopharmaceutical company. Our teams combine leading drug discovery capabilities and world-class R&D with the purpose of turning breakthrough science into life-changing medicines. 

We recognize that the difference in our team is our strength and are committed to creating an inclusive environment for all employees. Successful candidates must demonstrate inclusive behaviors in working with a different group of scientists to drive our core mission. 

Key Responsibilities 

• Create de novo therapeutic proteins using structure-guided generative AI and machine learning-based protein design and engineering technologies. 

• Integrate AI/ML protein design methods with structural biology and high-throughput experimental screening data to devise and execute de novo protein design and optimization strategies. 

• Process and analyze experimental functional data in context of protein structure, and optimize workflows using data for hit-to-lead optimization. 

• Evaluate and improve computational protein design strategies, methods and models (zero- and few-shot). 

• Train ML models to integrate structural data with experimental datasets to advance therapeutic programs. 

• Collaborate with laboratory scientists to design experiments that produce high-quality, ML-ready data. 

• Foster a high-performance culture of collaboration, engagement, self-accountability and inclusion. 

• Effectively partner across multidisciplinary interfaces to achieve organizational objectives. 

• Assess external advancements in the relevant scientific fields. 

 

Qualifications & Experience 

• Ph.D. in Biochemistry, Computational Biology, Protein Engineering, Physics, Bioengineering, Computer Science, Molecular Biology, Chemistry, Pharmaceutical Science, or a related STEM field and a minimum of 0-3 years of industry experience, or MS and 4+ years industry experience, or B.S. 7+ years industry experience. 

• Demonstrated success generating de novo proteins with desired in vitro behavior. 

• Extensive expertise in GenAI/ML-based protein design methods and protein structural biology. 

• Experience using experimental data to optimize protein sequences for function. 

• Proven industry track record of success working with cross-functional teams. 

• Commitment to scientific excellence and rigor. 

• Excellent communication and collaboration skills. 

• Champion for different and inclusive culture. 

• Strong external reputation with high-impact publications, presentations, and scientific community engagement. 

• Passion for sharing knowledge and helping colleagues develop. 

 

Required Skills:  

• Expert-level knowledge of structure-based generative AI methods for protein design and engineering, including de novo design, lead optimization and in silico prediction (e.g., RFdiffusion, Boltzgen, and/or BindCraft in combination with ProteinMPNN and/or AlphaFold). 

• Strong hands-on experience applying experimental data (e.g., affinity, stability, solubility) to optimize protein sequence/structure/function. 

• Strong skills in data analysis and visualization. 

• Comprehensive scientific knowledge across workflows and domains integral to the discovery of protein therapeutics. 

 

Preferred Skills 

• Deep understanding of protein structure and sequence representations, featurization and embeddings. 

• Demonstrated proficiency in computational protein design method/algorithm development. 

• Experience training/validating data-driven ML models to solve complex problems. 

 

#EligibleforERP

Required Skills:

Biopharmaceutical Industry, Biopharmaceuticals, Biopharmaceutics, Data Engineering, Design Applications, Drug Discovery Process, Generative AI, Inclusive Leadership, Inclusive Practices, Machine Learning (ML), Protein Design, Protein Engineering, Structural Biology, Systematic Problem Solving, Testing, Therapeutic Proteins, Workflow Optimization

Preferred Skills:

Current Employees apply HERE

Current Contingent Workers apply HERE

US and Puerto Rico Residents Only:

Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here if you need an accommodation during the application or hiring process.

As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics.  As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities.  For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

EEOC Know Your Rights

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We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another’s thinking and approach problems collectively.

Learn more about your rights, including under California, Colorado and other US State Acts

The salary range for this role is

$131,400.00 - $206,800.00

This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An employee’s position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs.

The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.

We offer a comprehensive package of benefits.  Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days. More information about benefits is available at https://jobs.merck.com/us/en/compensation-and-benefits.

You can apply for this role through https://jobs.merck.com/us/en (or via the Workday Jobs Hub if you are a current employee). The application deadline for this position is stated on this posting.

San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance

Los Angeles Residents Only: We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles’ Fair Chance Initiative for Hiring Ordinance

Search Firm Representatives Please Read Carefully 
Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company.  No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails. 

Employee Status:

Regular

Relocation:

Domestic

VISA Sponsorship:

Yes

Travel Requirements:

No Travel Required

Flexible Work Arrangements:

Not Applicable

Shift:

Not Indicated

Valid Driving License:

No

Hazardous Material(s):

n/a

Job Posting End Date:

08/10/2026

*A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.