Staff Software Engineer, Machine Learning and Computational Chemistry

Eikon Therapeutics • Millbrae, CA

4d • $200,000 - $241,500 • Onsite

About The Position

As part of Eikon’s diverse team, you will interface with biologists, chemists, microscopists, and optical and automation engineers to design and deploy computational solutions that enable the exploration and quantification of Eikon’s high-content datasets. You are an adventurous, passionate, and creative software engineer eager to apply your talents to empower interdisciplinary scientific exploration, inaugurate a radical drug-discovery paradigm, and ultimately create novel medicines. You will bring enthusiasm, energy, intellectual curiosity, and scientific rigor to this challenge.

Requirements

• Bachelor's Degree with 7 years of relevant experience or a Master’s degree with 5 years of relevant experience in Computer Science, Software Engineering, or a PhD with 2+ years of experience; or equivalent work experience
• Strong background in machine learning, statistics, data analysis techniques and chemistry and chemical terms/concepts.
• Strong programming expertise required with proficiency in languages such as Python, C, C++, etc.
• Experience with cheminformatics fundamentals, including molecular representations, molecular fingerprints, and the tools and libraries used to analyze and manipulate chemical structures (e.g., RDKit, OpenBabel).
• Practical and theoretical understanding of computational chemistry methods including docking, MD (Molecular Dynamics), FEP (Free Energy Perturbation), and retrosynthetic prediction applied to early drug discovery programs.
• Ability to efficiently investigate and solve problems, from prototype development to production designs.
• Excellent organizational, verbal, and written communication skills.
• Team-oriented, flexible, able to adapt to rapidly evolving goals and challenges.

Nice To Haves

• Strong Python programming expertise highly preferred.
• Familiarity with biology and biological terms/concepts at the college freshman level preferred.

Responsibilities

• Design and optimize algorithms and models for chemical property prediction, compound screening, and reaction optimization.
• Deploy computational chemistry tools into production pipeline environments and ensure scalability, reliability, and performance.
• Collaborate on computational chemistry pipelines to accelerate early drug discovery with simulation, modeling, and AI.
• Work collaboratively with scientists and engineers to understand tactical needs, prototype, and then productionize software to keep experiments moving forward.
• Work on multiple projects simultaneously, developing milestones and deadlines in coordination with the broader company goals.

Benefits

• 401k plan with company matching
• Medical (premiums covered by Eikon at 95%), dental and vision insurance (premiums covered by Eikon at 100%)
• Mental health and wellness benefits
• Weeklong summer and winter holiday shutdowns
• Generous paid time off and holiday policies
• Life/AD&D Insurance (premiums covered by Eikon at 100%) and optional supplemental employee-paid life/AD&D policies
• Enhanced parental leave benefit
• Daily subsidized lunch program when on-site

What This Job Offers

• Job Type: Full-time
• Career Level: Senior