Applications Scientist, Structural Biology

Applications Scientist, Structural BiologyAbout High Q Technologies

High Q Technologies builds FATHOM, a quantum-enabled electron paramagnetic resonance (EPR) platform that measures which conformational states a protein populates in solution, and in what proportions. Structure prediction, cryo-EM and crystallography tell you what a protein can look like. FATHOM tells you how often it looks that way, and how a drug candidate changes the balance.

We work with AI drug discovery companies, pharmaceutical and biotechnology companies, and academic laboratories. Most of that work runs as scientific projects: our team designs and runs the experiment that answers a partner's question about their own target. Some partners also install a FATHOM system in their own laboratory.

Our patented technology applies microwave quantum optics, developed from experimental quantum computing research in collaboration with Professor David Cory's group at the University of Waterloo, to make EPR far more sensitive. High Q is backed by Quantum Valley Investments and BlackBerry co-founders Mike Lazaridis and Doug Fregin. The company is headquartered in Waterloo, Ontario.

The Role

We are hiring an Applications Scientist with a structural biology background to be the scientific partner our customers work with, from the first conversation about their target to the result they act on. You do not need EPR experience. You need to understand proteins as moving, multi-state molecules, and to learn quickly how a distance measurement between two labelled sites can show which states are present and in what proportions.

Most of your time will go to AI drug discovery companies and pharmaceutical and biotechnology companies working with us on measurement projects and longer research partnerships. Their questions usually fall into two kinds:

• Mechanism. How does a compound change the states a target populates? Does a designed molecule do what it was designed to do?
• Ground truth. How well do the state populations a computational model predicts match what the protein actually does in solution?

You will also support customers who operate a FATHOM system in their own laboratory, helping them design experiments and interpret results.

Reports to: Principal Scientist

Location: Waterloo, Ontario

Key responsibilities

Design the experiment with the customer

• Work with a partner's structural, computational and medicinal chemistry scientists to turn their question into an experiment that can answer it: which sites to label, which constructs and conditions, which controls, and what a result would and would not show.
• Read a partner's published and disclosed work to find the question their programme actually holds and frame our proposal around it.
• With computational and machine learning teams, define how measured state populations will be compared with model predictions, and what a useful validation set looks like.

Deliver projects

• Plan and coordinate sample supply. Some partners provide their own protein; others have no wet laboratory, so you will specify constructs, cysteine mutants and labelling strategy, and manage work with contract protein production partners.
• Work with our EPR scientists to plan and run measurements, then analyse and interpret the resulting distance distributions in light of the available structures and models.
• Present results to partner teams in their own terms, including what the data support, what they do not, and what to measure next.
• Capture what each project leaves behind (constructs, reagents, protocols, experimental designs) so the next project on a similar target starts further ahead.

Support system customers

• Help customers who own a FATHOM system design experiments, prepare samples and interpret results.
• Contribute to training, application notes and user documentation written for scientists who are not EPR specialists.

Build the scientific case

• Lead or contribute to publications, application notes and conference presentations from project and partner work.
• Support grant applications with academic collaborators, including experimental design and preliminary data.
• Keep current with structural biology, structure and ensemble prediction, and drug discovery, and bring what customers are asking for back to our R&D and product teams.
• Join the commercial team in scientific conversations with prospective partners, including scoping calls and visits.

Required qualifications

• PhD or equivalent in structural biology, biophysics, biochemistry or a related field, with postdoctoral or industry experience.
• Hands-on experience solving or analysing protein structures by at least one of cryo-EM, X-ray crystallography, NMR, or integrative and hybrid methods.
• A working understanding of protein conformational dynamics: how proteins such as transporters, channels, receptors and kinases move between functional states, and how ligands shift that balance.
• Bench experience in protein biochemistry: construct design, site-directed mutagenesis, expression, purification and quality control.
• Comfort with structure prediction and molecular modelling outputs (for example AlphaFold-class models or molecular dynamics) and the ability to judge what they do and do not show.
• Evidence that you learn new techniques quickly and apply them independently.
• Clear scientific writing and presentation, for both specialist and non-specialist audiences.
• Willingness to travel, including internationally, to meet customers and partners.

Preferred qualifications

• Experience in a pharmaceutical, biotechnology or AI drug discovery company, or in an industry-facing core facility or contract research setting.
• Knowledge of the drug discovery process, including hit-to-lead and lead optimisation, mechanism of action studies and allosteric modulation.
• Experience with membrane proteins or large complexes.
• Any exposure to EPR, DEER/PELDOR, FRET, hydrogen-deuterium exchange mass spectrometry, or other solution methods that report on conformational states.
• Experience with site-directed spin labelling or other site-specific labelling chemistry.
• Python or similar for data analysis, and familiarity with structure visualisation and analysis tools.
• A publication record in structural biology or biophysics.
• Experience working directly with external collaborators or customers to scope and deliver projects.

What success looks like in your first year

1. First three months. You understand how a FATHOM measurement works and what a distance distribution can and cannot tell you, and you have taken part in live customer projects alongside our EPR scientists.
2. By six months. You lead the experimental design for new projects, from the scoping call to an agreed plan, and you are the main scientific contact for at least one partner.
3. By twelve months. Partners rely on you to explain what their results mean for their programme. Your project work has produced at least one application note, presentation or manuscript, and reusable constructs or protocols that shorten the next project on a similar target.

Location, compensation and how to apply

• Location: Waterloo, Ontario, with regular travel to customers, partners and conferences.
• Employment type: Full-time, permanent.
• Compensation: $80,000 - 110,000 annually dependent on experience
• Vacancy: This posting is for an existing vacancy.

How to Apply

Please submit your application through Employment Hero, including your CV and a cover letter. In your cover letter, please describe a protein whose conformational behaviour you have studied and explain what you would want to measure about it next.

High Q Technologies may use artificial intelligence-assisted tools to support administrative aspects of the recruitment process, including application review. Final hiring decisions are made by human decision-makers.

High Q Technologies is committed to fostering an inclusive, accessible, and barrier-free workplace and recruitment process. Accommodation is available on request at any stage of the recruitment and selection process. Applicants requiring accommodations are encouraged to advise us at any time.