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 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 research laboratories as needed. Qualifications Education: Bachelor's (with 7+ years experience), Master’s (with 4+ years experience) or Ph.D. in Protein Engineering, Biochemistry, Biophysics, Bioinformatics, Bioengineering, Structural Biology, Computational Biology or a 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. Benefits We offer a comprehensive package of benefits, including medical, dental, vision, and other insurance benefits for employees and families, retirement benefits (401(k)), paid holidays, vacation, compassionate and sick days. Detailed benefits information is available at Compensation Salary Range: $144,800.00 – $227,900.00 Eligible for annual bonus and long‑term incentive, if applicable. Employment Information Location: San Francisco, California (US and Puerto Rico Residents Only) Job Posting End Date: 07/10/2026 Visa Sponsorship: Yes Relocation: Domestic/International Travel Requirements: 10% EEO Statement 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. Note on Fair Chance Ordinances 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. #J-18808-Ljbffr MSD