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. 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 & 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 & 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. Salary and Benefits Salary range: $144,800.00 – $227,900.00. The successful candidate will be eligible for annual bonus and long‑term incentive, if applicable. We offer a comprehensive package of benefits, including medical, dental, vision, healthcare and other insurance benefits (for employee and family), retirement benefits, 401(k), paid holidays, vacation, and compassionate and sick days. Equal Employment Opportunity 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. Learn more about your rights, including under California, Colorado and other U.S. State Acts. #J-18808-Ljbffr Merck & Co.