Postdoctoral Fellow: AI development for de novo protein design

The Bethel Lab uses a variety of computational and experimental techniques to explore protein ensembles and conformational change. Current projects focus on combining existing protein structure databases with physics based simulation and our own data generation pipeline to generate new deep learning models of protein physics and function. We are using these models to generate new therapeutics, biosensors and biomaterials. The Bethel Lab is an HHMI affiliated lab and thus has stable funding for the foreseeable future.

Responsibilities:

• Curation and development of experimental and simulation datasets.
• Pre-train and fine-tune deep learning networks for physics-informed protein design.
• Collaborate effectively with experimental biochemists in the Bethel Lab and other research groups within and outside UCSD.
• Supervise and train other researchers in computation and machine learning techniques.
• Prepare and write scientific manuscripts, patent and fellowship applications in collaboration with the principal investigator.
• Attend and present findings at internal, local and national meetings.

Base Qualifications:

• PhD in computational biophysics, bioinformatics, systems biology computer science, physics or related field.
• Publication record demonstrating experience pre-training and/or fine-tuning transformer or diffusion based neural networks including, but not limited to, RFdiffusion, Boltz1/2, Evo2, and Alphafold
• Skilled in python and pytorch
• Knowledge of statistical mechanics and structural biology

Preferred Qualifications:

• Experience running and processing molecular dynamics simulations
• Applicants with experience processing cryo-EM datasets are particularly encouraged to apply

Interested applicants should contact Professor Bethel by email (nbethel at ucsd dot edu) with a CV, a letter describing your research interests, and contact information for three references.

UC San Diego is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to excellence through diversity. All qualified applicants will receive consideration for employment without regard to gender, race, color, religion, sex, sexual orientation, national origin, disability, age or protected veteran status.