Merck & Co, Inc

Sr. Scientist, Generative Protein Design

Merck & Co, Inc • $131K — $206K *
Cambridge, MA 02139In-Person
Pharmaceuticals & Biotech
Less than 5 years of experience
Today
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Job Overview by Ladders

Qualifications

  • Ph.D. in a related STEM field with relevant industry experience or equivalent MS/B.S. with more years of experience.
  • Proven ability to generate therapeutic proteins with in vitro functionality.
  • Extensive knowledge in Generative AI and ML for protein design and structural biology.
  • Experience in using experimental data for protein optimization.
  • Track record of successful collaboration with cross-functional teams.
  • Strong commitment to scientific rigor and excellence.
  • Excellent communication and collaboration skills.

Responsibilities

  • Design de novo therapeutic proteins using advanced AI/ML techniques.
  • Integrate AI/ML with structural biology to optimize protein design strategies.
  • Analyze experimental data to improve protein function and workflows.
  • Enhance computational design strategies and models for protein development.
  • Train ML models to align structural and experimental data to support therapy development.
  • Collaborate with scientists to ensure quality in data production for ML.
  • Cultivate a culture of collaboration and accountability in the team.

Benefits

  • Opportunity to work with cutting-edge AI and ML technologies in protein engineering.
  • Engage in projects that have a meaningful impact on patients' health.
  • Collaborative work environment across multidisciplinary teams.
  • Company commitment to scientific excellence and a diverse culture.
Full Job Description
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.

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

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.

About Merck & Co, Inc

Schering-Plough Corporation is a major U.S.-based manufacturer of pharmaceuticals. It operates in three segments: Prescription Pharmaceuticals, Animal Health, and Consumer Health Care. Schering-Plough develops products targeting on allergy, cancer, hepatitis, cardiovascular, central nervous system, respiratory system, and more.  It was founded in 1851 by Ernst Christian Friedrich Schering as Schering AG in Germany. Schering-Plough manufactured several pharmaceutical drugs, the most well-known of which were the allergy drugs Claritin and Clarinex, an anti-cholesterol drug Vytorin, and a brain tumor drug Temodar. It also developed drugs targeting on central nervous system and the respiratory system. Schering Plough also owned and operated the major foot care brand name Dr. Scholl's and the skin care line Coppertone. These also became a part of the new company. Schering-Plough was a full member of the European Federation of Pharmaceutical Industries and Associations (EFPIA), a membership which is also maintained by the new Merck.

Merck & Co, Inc Careers

Join the visionary team at Merck & Co, Inc, a global leader in healthcare dedicated to advancing the world of medicine. As part of our professional community, you'll find dynamic job opportunities that foster innovation and leadership across various fields. Merck & Co, Inc is not just a company; it's a place where you can make a difference.

Work You’ll Do

At Merck & Co, Inc, we are committed to improving global health through groundbreaking research and innovative healthcare solutions. Our team is at the forefront of developing new therapies and vaccines that significantly impact public health worldwide. By joining us, you will collaborate with some of the brightest minds in the industry, using your skills to contribute to projects that save and improve lives around the globe.

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Whether you're seeking an internship, a graduate opportunity, or a professional position, Merck & Co, Inc offers a range of career paths in environments that promote rapid professional growth and development. Explore job opportunities in research, digital transformation, manufacturing, and more, all while benefiting from a culture that supports diversity and inclusion.

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Merck & Co, Inc is an ideal environment for those who lead with curiosity and the drive to innovate. Our leadership is committed to fostering a culture where inventive thinking and collaboration are encouraged, making it a perfect place for professionals who seek to make an impact through their work.

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With Merck & Co, Inc, you are not just getting a job; you're gaining access to unparalleled career development opportunities. Enhance your skills through diverse training programs, workshops, and continuous learning courses designed to help you grow at every stage of your career.

Benefits and Culture

We understand that our employees are our greatest asset, which is why we offer competitive benefits designed to support the health and well-being of you and your family. From comprehensive health care coverage and retirement plans to flexible working conditions and wellness programs, our benefits package is designed to meet the diverse needs of our team members.

Join Our Team

Ready to advance your career at Merck & Co, Inc? Search open positions that match your skills and interests. We are continuously hiring and looking for passionate, creative, and solution-driven team players. Prepare your resume, sharpen your interview skills, and become part of a company that's dedicated to making a difference.

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Learn more about Merck & Co, Inc
Size
68,000 employees
Market Cap
$282.6 billion
Industry
Pharmaceuticals & Biotech
Net Income
$7 billion
Founded
1668
5 Year Trend
+4.1%
Revenue
$47.9 billion
NASDAQ
MRK
* Ladders Estimates

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