Lead Scientific Developer – Biologics & Protein Design

Cadence Design Systems; Santa Fe (NM); On-site; USD 120,000 - 180,000; Full time

Job summary

OpenEye Scientific, in collaboration with Cadence Design Systems, seeks a PhD‑level computational chemist to advance cloud‑based biomolecular modeling and drug discovery tools. You will work on scalable C++/Python software, MD simulations, and AI‑driven methods in a cutting‑edge framework.

Based in Santa Fe, NM, this on‑site role requires collaboration with teams across academia and industry; you’ll deliver robust software, mentor colleagues, and push forward protein informatics and biologics

Qualifications

• PhD (or equivalent) in computational chemistry, structural biology, biochemistry, or related field.
• Strong software development skills with Python and C++, and a track record of robust software delivery.
• Experience with MD simulations and machine learning methods.

Responsibilities

• Work on challenging problems and help find practical solutions in biologics drug discovery.
• Develop scalable, cloud-based biomolecular modeling and analysis tools.
• Implement data-driven models using sequence and 3D structural data.
• Collaborate with OpenEye, Cadence, and industry partners on new methods and tools.
• Contribute to OpenEye’s biomolecular modeling and protein informatics technologies.

Skills

Python

Machine learning

Molecular dynamics

Software development

Team collaboration

Education

PhD in computational chemistry/structural biology/biochemistry or related field

Tools

OpenEye toolkits

AWS/cloud computing

Job description

Location: On-site in SantaFe, NM.

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.

What you’ll do

• Work on challenging problems and help find practical solutions that advance the field of computational biologics drug discovery
• Develop highly scalable and integrated solutions for biologics drug discovery in the cloud
• Develop data‑driven models using sequence and 3D molecular shape representations leveraging AI and physics‑based approaches
• Expand OpenEye’s biomolecular modeling and protein informatics technologies
• Collaborate with colleagues within our group, within OpenEye & Cadence, as well as within the broader pharmaceutical industry on developing new methods, tools, and solutions

What you should have

• PhD (or equivalent experience) in computational chemistry, structural biology, biochemistry, or related field with at least 5 years relevant experience
• Strong desire to change the field of biologics drug discovery through hard work, creating robust software tools, and critical scientific evaluation
• Demonstrated ability to work both independently and as part of a team
• Ability to work humbly with others, admitting mistakes and constructively working through differences in opinion
• Experience with molecular dynamics simulations and machine learning
• Programming expertise, ideally in Python, preferably with experience using AI coding agents
• Proven track record of delivering software solutions

PLUS (not required)

• Expertise with traditional machine learning and/or modern deep learning methods
• Experience with OpenEye software/toolkits or other computational chemistry toolkits
• Experience with protein language models and protein folding technologies
• Experience with modeling antibodies based on sequence and structural data