Associate Scientist, Postdoctoral Fellow – Computational Protein Design

Merck; Cambridge (MA); On-site; USD 82,000 - 92,000; Full time

Job summary

Merck's Discovery Biologics in Cambridge, MA seeks a postdoctoral scientist to push boundaries in computational protein engineering and next-generation biotherapeutics design using state-of-the-art AI/ML and physics-based modeling. You will explore ensemble-aware design to impact therapeutic pipelines and develop tools for rapid data generation and validation.

The role emphasizes high-impact science, external publication opportunities, and collaboration within a Disruptive Technology group.

Qualifications

• PhD in Computational Biology, Bioinformatics, CS, Biophysics, Computational Chemistry, ML or related quantitative field.
• PhD or expected by Spring 2027.
• Experience applying computational protein design tools and structure prediction.

Responsibilities

• Implement benchmarking strategies for design approaches.
• Develop ensemble-aware generative design and scoring methods.
• Publish findings and share models and tools internally.

Skills

Python

ML frameworks

JAX

Team collaboration

Scientific communication

Education

PhD in Computational Biology or related

Tools

RFdiffusion

BoltzGen

ProteinMPNN

AlphaFold/Boltz/ESMFold

Job description

Job Description

Our company's Discovery Biologics is seeking a talented postdoctoral scientist motivated to push the boundaries of computational protein engineering and next-generation biotherapeutics design. In this role, you will develop and apply state-of-the-art artificial intelligence (AI) and machine learning (ML) tools in conjunction with physics-based modeling to address fundamental challenges facing computational protein design and structure prediction. The successful candidate will explore how ensemble-aware computational protein design (e.g. target conformational flexibility, state selectivity, multi-state binder design) can directly impact therapeutic pipelines and develop the methodology and tools to realize these unique advantages. Embedded in the Disruptive Technology group in our Cambridge, MA facility, the candidate will leverage our company's state-of-the-art capabilities and expertise in computational design, high-throughput production, and characterization for rapid data generation and model validation.

Job Description

Our company's Discovery Biologics is seeking a talented postdoctoral scientist motivated to push the boundaries of computational protein engineering and next-generation biotherapeutics design. In this role, you will develop and apply state-of-the-art artificial intelligence (AI) and machine learning (ML) tools in conjunction with physics-based modeling to address fundamental challenges facing computational protein design and structure prediction. The successful candidate will explore how ensemble-aware computational protein design (e.g. target conformational flexibility, state selectivity, multi-state binder design) can directly impact therapeutic pipelines and develop the methodology and tools to realize these unique advantages. Embedded in the Disruptive Technology group in our Cambridge, MA facility, the candidate will leverage our company's state-of-the-art capabilities and expertise in computational design, high-throughput production, and characterization for rapid data generation and model validation.

As a postdoctoral fellow, your focus will be to deliver broadly relevant, high-impact science and computational models and tools. Publication of this work in peer-reviewed journals and scientific conferences is expected and the scope of the research project is designed specifically for external publication opportunity.

Key Responsibilities

• Implement rigorous benchmarking strategies for evaluating state-of-the-art computational protein design approaches.
• Develop and validate ensemble-aware generative design and scoring methodologies for the advancement of next-generation biotherapeutics.
• Communicate findings within our company and the broader scientific community by authoring high-impact manuscripts and distributing high-quality models and tools.

Education Requirements

• Must currently hold a PhD OR
• Receive a Ph.D. no later than spring 2027
• Ph.D. in Computational Biology, Bioinformatics, Computer Science, Biophysics, Computational Chemistry, Machine Learning, or a related quantitative discipline.

Required Experience And Skills

• Hands-on experience developing and/or applying computational protein design tools (e.g., RFdiffusion, BoltzGen, ProteinMPNN) and structure prediction algorithms (e.g., AlphaFold, Boltz, ESMFold) for binder design. Understanding of relevant experimental techniques for evaluation and characterization.
• Quantitative evaluation mindset with a demonstrated ability to construct rigorous benchmarks, curate high-quality datasets, and apply critical-thinking and analytical skills for evaluation.
• Strong proficiency in Python and modern ML frameworks (e.g., PyTorch, JAX), alongside experience with high-performance computing and reproducible software development.
• Demonstrated commitment to collaboration in highly-interdisciplinary environments.
• Strong track record of clear and effective scientific communication in addition to first-author peer-reviewed publications and presentations at major conferences.

Preferred Experience And Skills

• Experience training or fine-tuning generative models (diffusion, flow-matching, etc.) or foundation models is highly desireable.
• Experience with conformational ensemble generation and analysis — ensemble prediction methods (e.g., AF-cluster, AlphaFlow, BioEmu) and/or molecular dynamics tools (e.g., AMBER, Desmond, GROMACS, OpenMM).
• Familiarity with energetic and free-energy methods for protein–protein interfaces (e.g., Rosetta/PyRosetta, Flex ddG, FEP).
• Experimental experience is a plus but not required. Familiarity with protein production, display technologies, and NGS-based selections with an understanding of how experimental data informs model development is advantageous.

Salary and Compensation

The salary range for this role is: $82,000-$92,000

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

Required Skills

Biophysics, Computational Biology, Computational Biophysics, Computational Methods, Machine Learning (ML), Protein Structure Modeling, Protein Structure Prediction

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

Requirements

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.

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Employee Status

Regular

Relocation:

Domestic

VISA Sponsorship

Yes

Travel Requirements

10%

Flexible Work Arrangements

Not Applicable

Shift

Not Indicated

Valid Driving License

No

Hazardous Material(s)

N/A

Job Posting End Date

10/26/2026

• 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.

Requisition ID:

R421434