Principal Scientist, Computational Protein Engineering

Job Description

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 8+ years) in computational protein biology, structural biophysics or related disciplines and relevant industry 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

#EligibleforERP 

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 Model

Effective 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

$172,700.00 - $271,900.00

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):

No

Required Skills:

3D Modeling, Antibody Therapeutics, Biologics, Computational Structural Biology, Detail-Oriented, Drug Discovery Process, Machine Learning, Molecular Biology, Protein Engineering, Protein Modeling, Protein Structure, Protein Structure Prediction, Structural Modeling

 Preferred Skills:

Job Posting End Date:

07/31/2025

*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.