Scientific Software Developer II – Modeler

Over the last eight years, Open Eye 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.

Open Eye, 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.

Open Eye, 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 Open Eye’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 Open Eye’s scientific and technical teams.

• 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.

• 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

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

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