Senior Scientist - Principal Scientist, Computational Chemistry

Superluminal Medicines Inc.; Boston (MA); On-site; USD 90,000 - 130,000; Full time

Benefits offered by this job

Comprehensive benefits package

401(k) match program

Massachusetts transportation subsidy

Unlimited paid time off

Disability insurance

Life insurance

Job summary

Superluminal Medicines Inc. in Boston is looking for a high-impact Computational Chemist to join the integrated discovery team. This role involves combining physics-based modeling, machine learning, and structural biology to drive small molecule drug discovery.

Key responsibilities include prioritizing compounds, collaborativing with interdisciplinary scientists, and designing workflows to optimize discovery cycles. Superluminal offers a competitive benefits package, including medical, dental, and vision insurance, along with unlimited paid time off.

Qualifications

• 1-3+ years of experience in a biotech or pharma setting performing computational support for drug discovery.
• Advanced knowledge of physics‑based and ML computational chemistry packages.
• Exceptional ability to communicate the scientific rationale behind designs.

Responsibilities

• Integrate physics-based simulations with ML predictions to prioritize compounds.
• Collaborate to develop actionable hypotheses and design computational experiments.
• Design chemical matter aimed at key program milestones.

Skills

Expert level use of structure‑based small molecule drug discovery software tools

Ability to work directly in a Linux‑based environment

Python scripting and prototyping experience

Education

Ph.D. in Computational Chemistry, Biophysics, or a related field

Tools

Schrodinger suite

OpenEye

MOE

RDKit

scikit‑learn

numpy

pandas

pytorch

Job description

About Superluminal Medicines

Superluminal Medicines is a generative biology and chemistry company revolutionizing the speed and accuracy of how small molecule medicines are created. The Company's platform aims to create candidate-ready compounds with unprecedented speed using a combination of deep biology, computational and medicinal chemistry, machine learning, and proprietary big data infrastructure. We are expanding the team of talented scientists who seek to build the future of small molecule drug discovery with creativity and innovation.

About the Role

We are seeking a high‑impact Computational Chemist to join our integrated discovery team. In this role, you will be the computational engine of our programs, combining physics‑based modeling, machine learning, and structural biology to generate quantitative predictions and develop necessary workflows to drive small molecule drug discovery. You will serve as a core strategic partner to medicinal chemists and biologists, focusing on compound design and tool development to impact the discovery pipeline and address unmet computational needs.

Key Responsibilities

• Integrate physics‑based simulations with ML predictions to achieve the quantitative accuracy required to prioritize compounds for synthesis
• Collaborate with a team of interdisciplinary scientists to develop actionable hypotheses and design computational experiments
• Design and prioritize chemical matter specifically aimed at hitting key program milestones, such as establishing in vivo POC, achieving selectivity windows, or optimizing ADMET profiles for candidate selection
• Develop, validate and deploy computational workflows to optimize the "Design‑Make‑Test‑Analyze" cycles and address gaps

Required Qualifications

• Ph.D. in Computational Chemistry, Biophysics, or a related field
• 1‑3+ years of experience in a biotech or pharma setting performing computational support for small molecule drug discovery
• Advanced knowledge of physics‑based and ML computational chemistry packages including knowing when and how to deploy various tools for maximum project impact
• Exceptional ability to communicate the "why" behind a design to a diverse scientific audience
• Design experience working in concert with medicinal chemistry teams to design synthesizable compounds that efficiently work towards defined goals of activity, affinity, selectivity, properties, etc.
• A proven track record for innovation in structure‑based small molecule drug discovery including developing and validating new workflows and techniques or expansions of existing ones

Preferred Qualifications

• Experience working with structural biology teams to extract the most information possible from cryo‑EM and x‑ray crystallography experiments and using this to accelerate programs using structure‑based drug discovery techniques
• Proven experience using ML to scale physics‑based insights, specifically in the context of large‑scale virtual screening or FEP‑guided lead optimization
• A proven track record for innovation in structure‑based small molecule drug discovery including developing and validating new workflows and techniques or expansions of existing ones

Skills & Competencies

• Expert level use of structure‑based small molecule drug discovery software tools including protein preparation, docking, FEP, QM, conformer selection (Schrodinger suite, OpenEye, MOE, etc.)
• Ability to work directly in a Linux‑based environment
• Familiarity with cloud computing infrastructure (AWS, GCS) is a plus
• Python scripting and prototyping experience including knowledge of key packages (RDKit, scikit‑learn, numpy, pandas, pytorch, etc.)

Benefits

Superluminal offers a comprehensive benefits package that fully covers employees' annual deductibles and monthly premiums for medical, dental, and vision insurance. The package also includes a 401(k) match program, a Massachusetts transportation subsidy, equity, unlimited paid time off, and both disability and life insurance.

Equal Opportunity Statement

Superluminal Medicines is an Equal Opportunity Employer committed to a culturally diverse workforce. All qualified applicants will receive consideration for employment without regard to race, color, creed, religion, national origin, age, ancestry, nationality, marital, domestic partnership or civil union status, sex, gender, gender identity or expression, affectional or sexual orientation, disability, veteran or military status or liability for military status.