Scientific Software Developer II – Modeler

Cadence Design Systems

1d•Onsite

About The Position

Over the last eight years, OpenEye Scientific has developed the field’s most advanced large-scale compute platform, Orion, built on Amazon Web Services. In this position, you will be working at the cutting edge of cloud computing, C++/Python development, and advanced MD simulation techniques. Your work will have the potential to make a major impact in drug discovery, and will be available to many pharmaceutical and biotech companies. 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.

Requirements

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

Nice To Haves

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

Responsibilities

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.