Scientific Software Developer II – Modeler (R54421/hm)

OpenEye, Cadence Molecular Sciences; Santa Fe (NM); On-site; USD 70,000 - 90,000; Full time

Job summary

OpenEye, Cadence Molecular Sciences located in Santa Fe, N.M. seeks a Computational Chemist to advance drug design and molecular modeling using the Orion platform. The role focuses on developing scalable workflows and machine learning models for binding free energy calculations. Candidates should possess a PhD in a relevant field and programming skills, preferably in Python. The position offers the opportunity to collaborate with scientific teams while addressing industry challenges. Join us in solving complex problems with innovative solutions.

Qualifications

• PhD (or equivalent) in computational chemistry, chemistry, or related field with 0 – 5 years of relevant experience.
• Knowledge of molecular dynamics simulations and binding free energy calculations.
• Experience in designing hypothesis-driven computational experiments.

Responsibilities

• Develop highly scalable workflows for relative binding free energy workflows in lead optimization.
• Explore machine learning models using large-scale relative binding free energy calculations.
• Work on retrospective and prospective projects to validate methodologies.

Skills

Molecular dynamics simulations

Binding free energy calculations

Programming expertise in Python

Machine learning

Team collaboration

Education

PhD in computational chemistry or related field

Tools

OpenEye software/toolkits

Job description

At Cadence, we hire and develop leaders and innovators who want to make an impact on the world of technology.

OpenEye, Cadence Molecular Sciences – a division of Cadence Design Systems – is an industry leader in computational molecular design through rapid, robust, and scalable software, consulting services, and Orion®, the only cloud‑native fully integrated software‑as‑a‑service molecular modeling platform. Combining unlimited computation and storage with powerful tools for data sharing, visualization and analysis in a customizable development platform, Orion offers unprecedented capabilities for the advancement of pharmaceuticals, biologics, agrochemicals, and flavors and fragrances.

OpenEye, Cadence Molecular Sciences is headquartered in Santa Fe, N.M., with offices in Boston, Mass.; Cologne, Germany; and Tokyo, Japan.

We are looking for a Computational Chemist to join our team of experts in drug design, molecular modeling, and free energy calculations. This highly focused team will work together to drive forward technology which leverages OpenEye’s Orion platform to better enable scientists in the pharmaceutical industry working on projects from lead development to clinical candidate selection. This role will require interactions with customers and OpenEye’s scientific and technical teams.

What you’ll do:

• Develop highly scalable and integrated workflows for relative binding free energy workflows in lead optimization
• Explore machine learning models such as 3D‑QSAR using large‑scale relative binding free energy calculations
• Develop data‑driven models using 2D cheminformatics and 3D molecular shape representations
• Work on retrospective and prospective projects both internally and with collaborators to validate methodologies.
• Work with Orion project team to further optimize compound design workflows in Orion.

What you should have:

• PhD (or equivalent experience) in computational chemistry, chemistry, or related field with 0 – 5 years relevant experience
• Knowledge of molecular dynamics simulations, binding free energy calculations, protein‑ligand interactions, or machine learning
• Experience in designing hypothesis‑driven computational experiments, and data‑driven decision making
• Programming expertise, ideally in Python, preferably with experience using AI coding agents
• Experience in or desire to learn about the pharmaceutical industry
• Strong desire to learn about customer problems and find practical solutions
• Demonstrated ability to work both as part of a team and independently

The following are a PLUS, but not required:

• Experience with OpenEye software/toolkits
• Expertise with traditional machine learning and modern deep learning methods
• Experience with synthetically accessible, pharmaceutically relevant generative chemistry

We’re doing work that matters. Help us solve what others can’t.