Director, Computational Protein Engineering
We are seeking an exceptional computational protein engineer to join the Discovery Biologics Protein Engineering department in South San Francisco to drive the advancement and application of computational antibody and protein designs and optimization in support of our biotherapeutic portfolio drug discovery programs.
The Principal Scientist, Computational Protein Engineering role will be a key contributor within the Protein Engineering Center of Excellence and the Discovery Biologics department as well as in project teams and therapy areas.
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 diversity of thought and experiences in our team are our strengths and we are committed to creating an inclusive environment for all employees. Successful candidates must demonstrate inclusive behaviors in working with our group of scientists to drive our core mission.
What you will do:
- Apply advanced protein structure prediction and modeling techniques to guide antibody and protein design and optimization
- Apply cutting-edge AI/machine learning models to support drug discovery and engineering projects
- Integrate with lab-based engineering workflow for accelerated design, make and test cycles
- Participate in cross-functional biologics programs from discovery to IND to achieve organizational objectives
- Thrive in a high-performance culture of collaboration, engagement, self-accountability, and inclusion
Qualifications:
Education:
- Bachelor's (with 14+ years), Master's (with 10+ years) or Ph.D. (with 6+ years) in computational protein biology, structural biophysics or related disciplines and relevant experience
Required Experience and Skills:
- Demonstrated experience applying computational modeling in protein and antibody drug design and engineering with a track record of key contributions to therapeutic progression
- Strong expertise in antibody and protein structure and physics-based computational tools such as Python, Rosetta, AlphaFold, protein MPNN
- Track record of scientific and technical excellence in computational protein engineering with demonstrated success in delivering optimized protein properties and complex functional designs
- Leadership of projects in protein and antibody therapeutics with strategic guidance to therapeutic programs
- Strong knowledge of antibody and protein therapeutics lab-bench workflows and demonstrated success in partnering with wet lab researchers in hit discovery and optimization
- Strong collaboration skills partner, with openness and agility to synergize with other computational team members within the department and across the organization
- Excellent verbal and written communication and collaboration abilities
- Experience working within a cross-functional and highly matrixed environment
- Ability to nurture, mentor and train scientists with varied levels of computational backgrounds
Preferred Experience and Skills:
- Experience in deep learning and generative modeling methods, AI/ML modeling, MD simulations, and large datasets
- Experience in broad antibody formats such as VHHs, multi-specifics, fusion proteins, and ADCs
The salary range for this role is $210,000.00 - $330,500.00.
Merck & Co., Inc. aspires to be the premier research-intensive biopharmaceutical company. They are at the forefront of research to deliver innovative health solutions that advance the prevention and treatment of diseases in people and animals.
Purpose:
We use the power of leading-edge science to save and improve lives around the world.
For more than 130 years, Merck has brought hope to humanity through the development of important medicines and vaccines. The company fosters an inclusive global workforce and operates responsibly every day to enable a safe, sustainable and healthy future for all people and communities.
January 21, 2026
5-7 business days
After submission
- •Explicit, repeated mentions of applied AI/ML methods and generative modeling (AlphaFold, protein MPNN, deep learning) indicate strong tool proficiency and innovation.
- •Role requires integration of computational models with lab 'design, make, test' workflows, demonstrating concrete workflow integration and automation potential.
- •Position provides strategic leadership and guidance in therapeutic programs, showing strategic application of AI to drive project and organizational outcomes.
This is a strong, high-fulfillment senior R&D role at a stable, well-known biopharma with explicit, competitive compensation and clear emphasis on cutting-edge computational protein engineering tied to therapeutic programs. Foundational needs (compensation and stability) are well signaled; the posting also supports belonging, esteem, and growth through cross-functional leadership, mentoring, and advanced technical challenges. Remaining gaps are: an inconsistent job title that should be clarified, limited explicit detail about benefits and formal development programs, and potential ambiguity around workload/expectations tied to the 'high-performance' culture and very broad skill requirements.
- •Title/role inconsistency: posting header lists 'Director, Computational Protein Engineering' but the body refers to 'Principal Scientist, Computational Protein Engineering' — unclear seniority, reporting, and expectations.
- •Ambiguous work–life boundary signal: phrases like 'thrive in a high-performance culture' and heavy cross-functional leadership expectations could imply high workload or long hours without explicit balance policies.
- •Very broad technical and domain expectations (physics-based modeling, AI/ML, MD, large datasets, deep wet-lab partnership, multiple antibody formats) — may indicate an unusually wide hiring bar or a role that expects both deep hands-on and broad management simultaneously.
- •Clear, competitive salary range ($210k–$330.5k) for a senior/director-level R&D role.
- •Employer is an established, research-intensive biopharmaceutical company with 130+ years of history—strong signal of organizational stability.
- •Role scope is high-impact: leadership of computational protein engineering applied to therapeutics, cross-functional project involvement, and mentoring responsibilities.
- •Can you describe the immediate team structure and direct reports for this role (size, disciplines, who this role reports to) and a typical cross-functional interaction cadence?
- •What does success look like in the first 6–12 months (key deliverables, KPIs, or program milestones) and how is impact measured for this position?
- •Can you clarify the hybrid/remote expectations (days in-office, flexibility, travel) and any policies supporting work–life balance for senior R&D staff?
Location
Salary Range
$210k - $331k
Employment Type
Full-time
Experience Level
Senior
Posted
October 23, 2025 (1 week ago)
3 Simple Steps
Prepare
Update your resume and write a tailored cover letter
Submit
Complete the online application form
Get Interviewed
Typically receive response within 5-7 business days
Documents Needed
Ready to apply?
Ensure you have all documents ready
💡 Mention you found this on Forward Future
