Associate Scientist, Post Doc Fellow- AI/ML & Computational Biology for Antigen Design

Scorpion Therapeutics; Pennsylvania; On-site; USD 65,000 - 95,000; Full time

Job summary

Scorpion Therapeutics seeks a Postdoctoral Scientist in AI/ML and computational biology for vaccine antigen design, focusing on structure-based conformational stabilization of viral proteins. Onsite in West Point, PA with about 10% travel.

You will develop and benchmark AI/ML workflows, integrate physics-based simulations with deep learning, collaborate with experimental teams, and publish findings at conferences. PhD in related field and biomolecular ML experience preferred.

Qualifications

• PhD in Computational Biology, Bioinformatics, CS, Biophysics, or related field (or completion by Spring 2027).
• Proven experience with ML models applied to biomolecular data (e.g., ESM, AlphaFold, ProteinMPNN).
• Proficiency in Python, ML frameworks (PyTorch, JAX), and high-performance computing; publication record.

Responsibilities

• Develop and benchmark AI/ML workflows for vaccine antigen design.
• Integrate physics-based simulations with deep learning.
• Collaborate with experimental teams for iterative model refinement.
• Publish scientific findings and present at conferences.

Skills

Python

ML for biomolecules

PyTorch

JAX

HPC

Publication record

Education

PhD in Computational Biology / Bioinformatics / CS / Biophysics

Tools

ColabFold

Rosetta

GROMACS

AMBER

Job description

Role

Postdoctoral Scientist specializing in AI/ML and computational biology for vaccine antigen design, focusing on structure-based conformational stabilization of viral proteins.

Responsibilities

develop and benchmark AI/ML workflows (protein language and folding models), integrate physics-based simulations with deep learning, collaborate with experimental teams for iterative model refinement, author scientific publications, and present research at conferences.

Requirements

PhD in Computational Biology, Bioinformatics, Computer Science, Biophysics, or related field (or completion by Spring 2027); proven experience with machine learning models applied to biomolecular data (e.g., ESM, AlphaFold, ProteinMPNN); proficiency in Python, ML frameworks (PyTorch, JAX), and high-performance computing; publication record.

Preferred

experience with structural modeling tools (ColabFold, Rosetta), molecular dynamics (GROMACS, AMBER), biophysical characterization methods, and conformationally dynamic protein complexes.

High-Value

focus on viral antigen design, structure stabilization, vaccine discovery, and integration of computational-experimental workflows.

Location

onsite West Point, PA with approximately 10% travel.

Collaboration

The role emphasizes industry-academic collaboration, cutting-edge AI/ML development for immunogen design, and multidisciplinary teamwork in infectious diseases and vaccine research.