Job DescriptionOur company's Discovery Biologics Disruptive Technologies is seeking an exceptional AI/ML protein engineer to drive the advancement and application of structure-based computational protein design and optimization methods to support our biotherapeutic portfolio. In addition to planning and executing experiments to improve and evaluate technical capabilities, 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 diversity 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 diverse group of scientists to drive our core mission.
In this role, a successful candidate will partner with computational and wet lab researchers to design experiments, identify and develop technologies, and create impactful medicines.
Key Responsibilities- Create novel biologic therapeutic proteins using structure-based generative AI and machine learning-based protein design and engineering technologies.
- Use cutting-edge AI and train ML models to integrate structural data with experimental datasets to advance therapeutic programs (e.g. NGS, affinity, stability, solubility)
- Improve computational strategies, methods and models (zero- and few-shot) by analyzing protein structure and experimental datasets.
- Devise and evaluate structure-based protein design strategies to create therapeutics.
- Collaborate with laboratory scientists to ensure 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- PhD and minimum of 0-3 years of industry experience, a M.S. and a minimum of 4 years of industry experience, or a BS and a minimum of 7 years industry experience.
- Extensive expertise with GenAI/ML-based protein design methods.
- Proven industry track record of success working with cross-functional teams.
- Commitment to scientific excellence and rigor.
- Excellent communication and collaboration skills.
- Champion for diverse 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.
- Experience training/validating data-driven ML models to solve complex problems.
- Deep understanding of protein structure and sequence representations, featurization and embeddings.
- Mastery of protein structural analysis and design tools (e.g. AlphaFold, Rosetta, RFDiffusion, protein MPNN, or similar)
- Strong skills in data analysis and visualization.
- Comprehensive scientific knowledge across workflows and domains integral to the discovery of protein therapeutics
Preferred skills- Strong hands-on experience creating and validating workflows to analyze NGS data sets for binder screening and affinity ranking.
- Expertise with bioinformatics tools and software for NGS data analysis: QC, statistical analysis, normalization, alignment, and variant calling.
- Demonstrated proficiency in computational protein design method/algorithm development.
#EligibleforERP
Required Skills: Artificial Intelligence (AI), Lead Optimization, Machine Learning (ML), Protein Design, Protein Engineering, Protein Modeling, Proteins, Protein Structure, Rosetta Studio, Structural Analysis
Preferred Skills: Next Generation Sequencing (NGS)
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:
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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
U.S. Hybrid Work ModelEffective September 5, 2023, employees in office-based positions in the U.S. will be working a Hybrid work consisting of three total days on-site per week, Monday - Thursday, although the specific days may vary by site or organization, with Friday designated as a remote-working day, unless business critical tasks require an on-site presence.This Hybrid work model does not apply to, and daily in-person attendance is required for, field-based positions; facility-based, manufacturing-based, or research-based positions where the work to be performed is located at a Company site; positions covered by a collective-bargaining agreement (unless the agreement provides for hybrid work); or any other position for which the Company has determined the job requirements cannot be reasonably met working remotely. Please note, this Hybrid work model guidance also does not apply to roles that have been designated as "remote".
The salary range for this role is
$128,800.00 - $202,700.00
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 ;br>
You can apply for this role through (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:12/8/2025
*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. 
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