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Molecular Modeling Jobs in Boston, MA (NOW HIRING)

System One

Biochemist/Molecular Biologist

Cambridge, MA · On-site

$35 - $41.82/hr

Contract Compensation: $35-$41.82 Work Model: Onsite - onsite Hours: 40.0 hours/week Overview Our clients BioMedicine Design (BMD) is seeking a highly motivated Biochemist/Molecular Biologist to join ...

System One

Biochemist/Molecular Biologist

Cambridge, MA · On-site

$35 - $41.82/hr

Contract Compensation: $35-$41.82 Work Model: Onsite - onsite Hours: 40.0 hours/week Overview Our clients BioMedicine Design (BMD) is seeking a highly motivated Biochemist/Molecular Biologist to join ...

System One

Biochemist/Molecular Biologist

Cambridge, MA · On-site

$35 - $41.82/hr

Contract Compensation: $35-$41.82 Work Model: Onsite - onsite Hours: 40.0 hours/week Overview Our clients BioMedicine Design (BMD) is seeking a highly motivated Biochemist/Molecular Biologist to join ...

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All JobsMolecular Modeling JobsMolecular Modeling Jobs in Boston, MA

Molecular Modeling information

See Boston, MA salary details

$11.9K

$87.7K

$112.4K

How much do molecular modeling jobs pay per year?

As of Sep 5, 2026, the average yearly pay for molecular modeling in Boston, MA is $87,658.00, according to ZipRecruiter salary data. Most workers in this role earn between $75,000.00 and $107,000.00 per year, depending on experience, location, and employer.

What is a molecular modeling?

A Molecular Modeling job involves using computer simulations and theoretical techniques to study molecular structures, interactions, and properties. Professionals in this field apply computational chemistry, molecular dynamics, and quantum mechanics to predict molecular behavior in drug discovery, materials science, and biochemistry. They work with specialized software and collaborate with experimental scientists to design and optimize compounds for various applications.

What are the key skills and qualifications needed to thrive in molecular modeling, and why are they important?

To thrive in Molecular Modeling, you typically need a strong background in chemistry, biochemistry, or a related field, with a solid understanding of molecular structures and computational methods. Experience with molecular modeling software such as Schrödinger, MOE, or Gaussian, as well as familiarity with scripting languages like Python, is highly valuable. Analytical thinking, problem-solving abilities, and effective communication are key soft skills for interpreting complex data and collaborating with interdisciplinary teams. These qualifications are crucial for accurately modeling molecular systems, advancing research projects, and facilitating successful teamwork in scientific environments.

What are the typical career advancement opportunities for someone in molecular modeling?

Molecular modeling professionals can pursue a variety of career advancement opportunities, including progressing to lead scientist or principal investigator roles, moving into project management, or specializing in areas like drug design or materials science. With experience, you may also transition into roles in academia, regulatory affairs, or scientific consulting. Continued professional development through advanced degrees, certifications, or technical workshops can further expand your options and responsibilities. Additionally, collaborating on interdisciplinary projects and publishing research can enhance your reputation and open doors to leadership positions in the field.

What are the most commonly searched types of Molecular Modeling jobs in Boston, MA?

The most popular types of Molecular Modeling jobs in Boston, MA are:

What are popular job titles related to Molecular Modeling jobs in Boston, MA?

For Molecular Modeling jobs in Boston, MA, the most frequently searched job titles are:

What job categories do people searching Molecular Modeling jobs in Boston, MA look for?

The top searched job categories for Molecular Modeling jobs in Boston, MA are:

Molecular Modeling jobs near you
Infographic showing various Molecular Modeling job openings in Boston, MA as of August 2026, with employment types broken down into 84% Full Time, 12% Part Time, and 4% Contract. Highlights an 83% Physical, 5% Hybrid, and 12% Remote job distribution, with an average salary of $87,658 per year, or $42.1 per hour.

Research Scientist, Molecular AI

Scorpion Therapeutics

Boston, MA • On-site

$140 - $210/hr

Other

Medical, Dental, Vision, Life, Retirement, PTO

Posted 6 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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