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Job Information

Pfizer Sr. Principal Scientist/Principal Scientist, Structure Based Protein Analysis in La Jolla, California


We are seeking a protein structure modeling expert to design industry-leading biotherapeutics as part of Pfizer's BioMedicine Design team. The successful candidate will join project teams to optimize protein-based therapeutic leads (such as antibodies, multi-specifics, and fusion proteins) in early through late discovery, primarily using protein structure, molecular simulation, and AI/ML property prediction models. The candidate will evaluate and create improved computational workflows, and collaborate across departments to generate and analyze high quality datasets to inform design of improved AI/ML prediction models. Other areas of opportunity in our group include AAV based gene therapy and RNA vaccine

optimization, and engineering improved protein scaffolds.


Works with project teams as a primary source of knowledge for structure-based computational analysis of protein biotherapeutic leads and provides optimized designs. Effectively communicates results and recommendations to colleagues with diverse scientific backgrounds. Evaluates/implements new or improved methods to increase throughput and/or accuracy of molecular modeling workflows. Analyzes data sets to discover relationships between protein structure and key pharmaceutical properties. Engineers improved general platforms for protein therapeutics, gene therapies, and RNA vaccines.


  • PhD in biochemistry, chemistry, or a related field and experience in the biopharmaceutical industry.

  • Strong track record of structure-based engineering of protein properties (such as stability and binding partner affinity).

  • Expertise in one or more commonly used protein structure modeling software packages.

  • Programming in a Linux environment using a scripting language such as Perl or Python.

  • Working knowledge of bioinformatics tools and databases.

  • Conducting research projects in a team setting, presenting results to scientists of varying technical backgrounds.


  • Working knowledge of antibody structure and function is a significant advantage.

  • Experience with computational RNA structure prediction and/or stabilization.

  • Linux systems administration skills and knowledge of HPC environments.

  • Knowledge of ML/AI methods.

  • Experience with one or more of the following software suites: Schrodinger, Rosetta, Discovery Studio, FoldX.

  • Experience integrating multiple scientific software toolkits to develop new analysis workflows usable by colleagues.

  • Strong track record of publication in topics involving protein structure analysis.

Other Job Details:

  • Eligible for Employee Referral Bonus: YES


Sunshine Act

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EEO & Employment Eligibility

Pfizer is committed to equal opportunity in the terms and conditions of employment for all employees and job applicants without regard to race, color, religion, sex, sexual orientation, age, gender identity or gender expression, national origin, disability or veteran status. Pfizer also complies with all applicable national, state and local laws governing nondiscrimination in employment as well as work authorization and employment eligibility verification requirements of the Immigration and Nationality Act and IRCA. Pfizer is an E-Verify employer.

Research and Development