Senior Specialist, Computational Protein Design

Job Description

We are seeking an innovative and experienced computational protein design scientist to join the Discovery Biologics Protein Engineering department. In this role, you will lead AI- and structure-guided protein design efforts, driving iterative design cycles from concept to candidate. As a functional subject matter expert, you will interface across Discovery Biologics, computational biology, and therapeutic area teams to shape and execute our AI-enabled protein design strategy.

We recognize that 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 group of scientists to drive our core mission.

What you will do:

• Familiar with the state-of-the-art generative models (e.g., RFDiffusion, ProteinMPNN, ESM3) and apply these protein design methods within iterative design–test–learn cycles; benchmark approaches against experimental outcomes to guide strategy.

• Apply physics-based and ML protein design tools (e.g., Rosetta, AlphaFold2), integrating structural and biophysical intuition to drive functional optimization of biologics, including antibodies, VHHs, bispecifics, and scFvs.

• Build AI-powered iterative design cycles that integrate high-throughput screening data and predictive models to improve hit rates, candidate quality, and speed to progression.

• Build computational workflows that further program goals, leveraging existing HPC/cloud resources and partnering with other of our company's Research Laboratories teams as needed.

QUALIFICATIONS:

Education:

• Bachelor's (with 7+ years), Master's (with 4+ years) or Ph.D. in Protein Engineering, Biochemistry, Biophysics, Bioinformatics, Bioengineering, Structural Biology, Computational Biology or related STEM field and relevant protein design experience

Required Experience and Skills:

• Hands-on experience with modern protein design tools (e.g., AlphaFold, Rosetta, RFDiffusion, ProteinMPNN, ESM, or equivalent), including generative models, model training, fine-tuning, large-scale inference, and performance evaluation in a research setting

• Proven ability to develop and benchmark computational pipelines for large-scale candidate generation and design library creation

• Strong protein biophysics intuition with a proven track record of optimizing expression, stability, affinity, and developability, and translating structural and biophysical insights into experimentally validated design outcomes

• Demonstrated track record through high-impact publications, conference presentations, or open-source contributions in computational protein design or a closely related field

• Excellent verbal and written communication and collaboration abilities

Preferred Experience and Skills:

• Deep understanding of protein biophysics and structure–function relationships, with the ability to quickly contextualize and adapt design strategies to new targets

• Expertise in functional optimization of biologics, especially antibodies

• Demonstrated proficiency in computational protein design method/algorithm development

• Prior hands-on wet lab protein engineering experience

#EligibleforERP 

Required Skills:

Antibodies, Biologics, Computational Biology, Computational Biophysics, Computational Design, Generative AI, Library Development, Model Training, Protein Design, Protein Engineering, Protein Structure, Rosetta Studio

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

EEOC GINA Supplement​

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

$144,800.00 - $227,900.00

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/International

VISA Sponsorship:

Yes

Travel Requirements:

10%

Flexible Work Arrangements:

Not Applicable

Shift:

1st - Day

Valid Driving License:

No

Hazardous Material(s):

n/a

Job Posting End Date:

07/10/2026

*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.