Research Software Engineer – Toronto

At ProteinQure, we have built the best computational platform for peptides that target extracellular targets. Our mission is to help create a world where drugs are engineered, not discovered. We work on treatments for cancer and other indications while also partnering with industry leaders in drug discovery to generate novel therapeutics outside of the conventional chemical space. Our technology combines computational biophysical models with statistical and machine learning approaches to enable us to search across vast spaces of protein therapeutics. We have worked with three of the top 25 pharma companies and have validated our tools on multiple targets. We also have multiple internal programs, the most advanced being a First-in-Class peptide drug conjugate for TNBC, which is in a Phase 1 clinical trial including the best sites in North America. A second clinical program is expected within 3 years. Our other internal programs focus on using peptides as delivery vehicles for therapeutic payloads such as radioisotopes and siRNA.

The Research Software Engineer is responsible for developing, maintaining, and supporting the software tools and computational workflows that enable ProteinQure’s drug discovery research. Working closely with scientists and engineers, they translate research needs into reliable, reproducible software, troubleshoot technical issues, and improve the performance and usability of the computational platform. The role combines hands-on software development with technical support for scientific users, along with ownership of scoped projects and contributions to testing, documentation, and shared engineering practices.

Key responsibilities include:

• Development, maintenance, and support for scientific computational workflows.
• Development of computational tools for protein property prediction and optimization.
• Scoping computational resource requirements for internal and external research projects.
• Collection of product requirements from scientists and translation into technical specifications.
• Supporting development of machine learning models.
• Participating in code reviews and shared engineering practices; taking ownership of scoped improvements from requirements through deployment and ongoing support.

Required Knowledge, skills and abilities:

• 3-5 years of software development experience.
• Proficiency in Python and experience maintaining software used by others, including debugging, testing, and dependency management.
• Experience using AI-assisted development tools, with independent review, testing, and validation of generated code and appropriate handling of confidential information.
• Familiarity with Linux environments, shell scripting, and troubleshooting software execution issues.
• Ability to prioritize development tasks alongside support requests, communicate tradeoffs, and recognize when to seek guidance.

[Nice-to-have]

• DevOps experience.
• Kubernetes experience.
• Experience with computer hardware / on-prem servers.

[Nice-to-have] Experience in cell, molecular or protein biology.

Excellent English communication skills, both verbal and written.

Legally able to work in Canada.