Scientific Developer Intern – Structural Biology

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

This internship will focus on building tools to compare simulations directly with data from Structural Biology experiments. OpenEye-CMS’s Weighted Ensemble simulation software enables efficiently enhanced exploration of protein conformational space though Molecular Dynamics (MD) simulation, allowing for new insights that accelerate and improve drug discovery efforts. You will help expand on this framework, building tools to guide Enhanced Sampling through direct comparison with experimental data. You will be tasked with building tools to produce volumetric datasets from experimental data, compare simulation with these data, apply these methods to Enhanced Sampling simulation, and extract information from these simulations that provide new insight into the experimental data and the system of interest. Expect to gain experience in a professional scientific software development environment, collaborate with working scientists from a variety of backgrounds in computational drug discovery, and build tools to enhance modeling efforts at OpenEye-CMS and beyond – as well as spend the summer in beautiful Santa Fe, New Mexico with a lovely group of fellow interns.

Key Learnings:

• Professional software development practices (testing and validation, version control, branching, and merging of code, bug fixing and anticipation, integration; etc.)
• Experience with state-of-the-art computational chemistry tools and platforms (Enhanced Sampling Molecular Dynamics, the OpenEye software suite, and the Orion Cloud Platform)
• Structural Biology modeling and interfacing with experimental data for validation
• Collaboration on a novel scientific software development project, with a world-class team.

What you should have (formally MUST HAVES/REQUIREMENTS):

• Graduate student in a relevant field of inquiry
• Introductory-to-Intermediate software development experience (specifically in Python; though experience with other languages like Java, Julia, Swift, C(++), etc. may suffice).
• Familiarity with undergraduate-level introductory biology, chemistry, and physics.

The following are a PLUS, but not required (preferred skills/experience):

• Familiarity with Structural Biology (specifically X-ray Crystallography).
• Experience with scientific software development in Python (numpy, scipy, matplotlib, pandas, etc.).
• Experience with Molecular Dynamics software (GROMACS, AMBER, NAMD, MDTraj, OpenMM, etc.).

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