Senior Computational Chemist, Drug Discovery

About the Role:

SandboxAQ’s AI Simulation team develops novel drugs and materials by integrating AI and physics-based computational solutions. Our AQBioSim group seeks a computational chemist who will not only apply cutting-edge methodologies but also critically assess and refine computational approaches. This individual will challenge assumptions, ask "why" when interpreting results, and ensure the reliability and accuracy of findings rather than blindly trusting outputs.

This role will drive innovation by combining quantum, AI, and physics-based methods—such as molecular dynamics and active learning free energy perturbation—to advance drug discovery. Working within a highly skilled and multidisciplinary team, including drug hunters with a strong track record in drug discovery, computational chemists, physicists, AI experts, and software engineers, you will play a key role in shaping the future of computational drug design.

What You’ll Do:

• Apply computational solutions to address unmet drug discovery challenges, questioning assumptions and rigorously validating results.
• Work closely with the development team to enhance SandboxAQ’s unique technology and Large Quantitative Models (LQMs) for large-scale impact.
• Apply SandboxAQ’s computational platform to provide high-value drug discovery solutions while critically evaluating its methodologies and results.
• Translate insights from molecular dynamics, free energy perturbation, molecular docking, quantum, and ML methods into actionable, testable drug discovery hypotheses.
• Collaborate closely with ML experts and cross-functional teams to prototype and scale innovative drug design solutions.
• Develop and deploy computational methods and workflows to generate and evaluate hypotheses, guiding design decisions and influencing project direction.
• Challenge conventional thinking by critically assessing and interpreting computational outputs, ensuring robust scientific conclusions.
• Directly contribute to the discovery of innovative medicines by integrating computational chemistry techniques into multidisciplinary drug discovery teams.
• Generate and evaluate hypotheses to assist design decisions and influence project direction by deploying and developing computational methods and workflows
• Attend regular meetings with The Ellison Medical Institute (EMI) in Los Angeles to support and advance SandboxAQ - EMI strategic collaboration

About You:

• PhD in computational physics, computational chemistry, or a related discipline.
• 3-5 years of relevant experience, including hands-on experience with computational chemistry applied to drug discovery in biotech, pharma, or related industries.
• Excellent communication skills and record of fostering successful internal collaboration and effective external partnerships
• A deep commitment to critical thinking - comfortable questioning methodologies, challenging assumptions, and refining approaches to improve predictive accuracy.
• A drive to cooperate with colleagues to identify problems and communicate technical solutions clearly and effectively.
• A hands-on mentality & comfortable with getting deep into the technical weeds of highly complex problems, and a track record of driving projects to completion
• Proficiency in structure-based drug design and familiarity with ligand-based drug design methods.
• Experience with GPU-accelerated MD codes like OpenMM.
• Experience in the Python data science stack (NumPy, Pandas, SciPy, etc.).
• Familiarity with ligand-protein free energy of binding prediction methods such as Free Energy Perturbation (FEP) or similar.
• Experience running computational chemistry/quantum simulations on high-performance computing (GPU) environments for corporate R&D, innovation labs, or academic research.
• A passion for solving scientific problems in chemistry and biology through computational and data-driven methods, with a commitment to rigorous validation and scientific integrity.
• Ability to leverage both experimental and computational data in forming strategic drug discovery approaches
• You live within the LA metro area and are willing to commute to the Ellison Medical Institute (EMI) at least once a week to support and advance SandboxAQ - EMI strategic collaboration

Preferred qualifications:

• Experience in peptide & antibody research
• Experience in quantum chemistry and/or protein folding
• Experience in drug discovery project management

The US base salary range for this full-time position is expected to be $158k - $221k per year. Our salary ranges are determined by role and level. Within the range, individual pay is determined by factors including job-related skills, experience, and relevant education or training. This role may be eligible for annual discretionary bonuses and equity.