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Sr. Principal Scientist/Principal Scientist, Structure Based Protein Analysis

La Jolla, California, United States;
Closing date
Jul 13, 2022

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Physical Sciences, Chemistry
Position Type
Full Time
Job Type
Staff Scientist
Organization Type
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Role Summary

Pfizer's BioMedicine Design (BMD) team is seeking a structure-based modeling & computational design expert to direct industry-leading biotherapeutic engineering research from early discovery through delivery to the clinic. Through team leadership, team membership, and mentoring/supervising junior colleagues, the successful candidate will collaborate to optimize therapeutic leads (such as antibodies, fusion proteins, and gene therapy constructs) and discover improved approaches to biotherapeutic design. The candidate will apply, evaluate, and create computational workflows for molecular simulation, design experiments, and analyze high quality datasets informing the development of improved AI/ML prediction models. Other areas of active research in our group include AAV based gene therapy, mRNA therapeutic design, and antibody/protein scaffold engineering.


As a project team lead, makes and communicates decisions based on input from team members with diverse scientific backgrounds. Works with other project teams across BMD as a primary source of knowledge for computational optimization of biotherapeutic leads. Conceives and leads implementation of new methods to increase throughput/accuracy of molecular modeling workflows, including through collaboration with AI/ML experts. Analyzes data sets to discover relationships between molecular structure and key pharmaceutical properties. Engineers improved general platforms for protein therapeutics, AAV gene therapies, and RNA vaccines. Manages/mentors junior colleagues in these skills.

  • PhD in biochemistry, chemistry, or a related field and experience in the biopharmaceutical industry.
  • Strong track record of structure-based protein engineering, including in a team leadership setting.
  • 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.

  • Experience mentoring or supervising junior colleagues.
  • Working knowledge of antibody structure and function.
  • 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


Pfizer requires all U.S. new hires to be fully vaccinated for COVID-19 prior to the first date of employment. As required by applicable law, Pfizer will consider requests for Reasonable Accommodations.

Sunshine Act

Pfizer reports payments and other transfers of value to health care providers as required by federal and state transparency laws and implementing regulations. These laws and regulations require Pfizer to provide government agencies with information such as a health care provider's name, address and the type of payments or other value received, generally for public disclosure. Subject to further legal review and statutory or regulatory clarification, which Pfizer intends to pursue, reimbursement of recruiting expenses for licensed physicians may constitute a reportable transfer of value under the federal transparency law commonly known as the Sunshine Act. Therefore, if you are a licensed physician who incurs recruiting expenses as a result of interviewing with Pfizer that we pay or reimburse, your name, address and the amount of payments made currently will be reported to the government. If you have questions regarding this matter, please do not hesitate to contact your Talent Acquisition representative.

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

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