Intern – Scientific Developer Target Exploration

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 leveraging the information contained in molecular dynamics (MD) simulations of proteins to generate insights into the properties of potential drug molecules. OpenEye, Cadence Molecular Sciences (OECMS) Weighted Ensemble Molecular Dynamics (WEMD) simulation software in the Orion cloud platform allows for efficient exploration of protein conformational space, which can be further analyzed to better understand a protein’s structure and dynamics and discover cryptic pockets. You will be tasked with building on these tools, with the goal of translating the information contained in the simulations to better understand the properties of molecules which bind to predicted pockets on the protein’s surface. Candidates should expect to gain experience in a professional scientific software development environment, be willing and excited to collaborate with working scientists from a variety of backgrounds in computational drug discovery, and to have the ability to build software tools to enhance modeling efforts at OECMS and beyond – as well as spend the summer in beautiful Santa Fe, New Mexico with a 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).
• Experience with 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:

• Graduate student or advanced undergraduate student in a relevant field of inquiry (Physics, Chemistry, Structural Biology, Computer Science).
• Introductory-to-Intermediate software development experience (specifically 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/Cryo-EM) or AI/ML protein structure prediction.
• Experience with scientific software development in Python (numpy, scipy, matplotlib, pandas, etc.).
• Experience with Molecular Dynamics software (GROMACS, AMBER, NAMD, MDTraj, OpenMM, etc.).