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Molecular Design Scientist Jobs (NOW HIRING)

Aragen

Scientist / Sr Scientist

Morgan Hill, CA · On-site

$101K - $138K/yr

Biologics Discovery & Molecular Biology * Design and optimize expression constructs and mammalian ... S. in a related scientific discipline with 12+ years of relevant industry experience.

Aragen

Scientist / Sr Scientist

Morgan Hill, CA · On-site

$101K - $138K/yr

Biologics Discovery & Molecular Biology * Design and optimize expression constructs and mammalian ... S. in a related scientific discipline with 12+ years of relevant industry experience.

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How much do molecular design scientist jobs pay per year?

As of Sep 14, 2026, the average yearly pay for molecular design scientist in the United States is $81,704.00, according to ZipRecruiter salary data. Most workers in this role earn between $62,500.00 and $92,000.00 per year, depending on experience, location, and employer.

What cities are hiring for Molecular Design Scientist jobs?

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For Molecular Design Scientist jobs, the most frequently searched job titles are:

Research Scientist, Molecular AI

Boston, MA • On-site

Scorpion Therapeutics
51 - 200 employees
Learn more about Scorpion Therapeuticsexternal

Other

Medical, Dental, Vision, Life, Retirement, PTO

Posted 15 days ago

Job description

About the role:

Research Scientist (AI-enabled drug discovery) focused on structure-guided small-molecule design.

How you will contribute:
  • Develop and iterate deep learning models across the molecular modeling stack (structure prediction, protein–ligand co-folding, affinity, and/or generative design).
  • Build benchmarking/evaluation pipelines linking offline metrics to real-world performance.
  • Integrate validated models into production-ready drug discovery workflows.
  • Apply computational and data-analysis methods to structural/sequence datasets to guide model development.
  • Use generative AI and predictive ML to design and prioritize chemical matter for research projects.
  • Communicate results via talks, technical write-ups, and peer-reviewed publications.
  • Collaborate with ML engineers, structural biologists, and software engineers to prototype/scale solutions.
Skill and qualifications (required):
  • Ph.D. in Computational Biology/Biophysics/CS/Computational Chemistry (or related), with ML focus in molecular modeling.
  • Hands-on deep learning development/training/validation; architectures (transformers, equivariant NNs, diffusion models).
  • Experience with modern structure prediction/co-folding (e.g., AlphaFold2/3, RoseTTAFold, Chai-1, Boltz) or comparable systems.
  • Python; PyTorch and/or JAX.
  • Scientific rigor; strong written/verbal communication; teamwork in multidisciplinary environments.
Preferred experience/skills:
  • Postdoctoral/industry experience in structure prediction or structure-based drug design.
  • Binding affinity prediction experience.
  • Publications/preprints (NeurIPS/ICML/ICLR).
  • Cloud deployment (GCP/AWS/Azure) and/or GPU/HPC; agentic coding tools (e.g., Claude Code, Codex).
Benefits (high level):
  • Medical/dental/vision
  • 401(k) match
  • disability and life insurance
  • tuition reimbursement
  • paid volunteer time off/holidays
  • sick time (up to 80 hours/year)
  • vacation (up to 120 hours for new hires)
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