Computational Scientist (Structural Bioinformatics)

Cyclica Inc.
Toronto, ON, Canada
Job Type:
  • Staff (Fulltime Permanent)
Degree Level Required:
Apply Now

Computational Scientist (Structural Bioinformatics)

Computational Scientist (Structural Bioinformatics) In expanding our R&D team, we are seeking a Computational Scientist with expertise in Structural Bioinformatics. Computational Scientists develop new scientific functionality, enhance ML models with new data or algorithms, and evaluate the quality of predictions. They are experts in their scientific domain and skilled programmers. This position is open to Ph.D. graduates that have experience working on projects analysing 3D models for thousands of proteins. The successful candidate is expected to understand details on the PDB file formats, such as altlocs, insertion codes, biological units, temperature factors, connectivity representations etc. The successful candidate will have guidance and mentorship from existing staff scientists with similar technical skillsets.

About Cyclica Cyclica is a Toronto-based, venture-backed biotechnology company that has recently been named by Deep Knowledge Analytics as one of the top 20 AI in Pharma companies globally. Cyclica provides its web-based drug discovery platform to world-class pharmaceutical, biotechnology, and academic partners to enable the development of safer and more effective medicines.

Our Stack:

  • Google Cloud Platform
  • Ubuntu Server
  • Python
  • Django
  • PostgreSQL
  • Redis
  • Javascript / React
  • Gitlab


  • Collaborate with peer computational scientists and software developers on tasks related to 3D representations of proteins.
  • Maintain and build upon databases of protein structure models, including data sanitization and automatic updaters.
  • Innovate new abstractions that efficiently encode information embedded in various facets of protein structures, including global topology, surfaces, interfaces, pockets, etc.
  • Collaborate with Cyclica’s Machine Learning team, providing new structural encoders tailored to new learning tasks.
  • Remain up to date on trends related to 3D protein models, including methods in structural bioinformatics.
  • Troubleshoot occasional problems associated with new proteins being integrated into our internal databases.
  • Troubleshoot predictive anomalies reported by clients and partners, related to unusual structural models.
  • Write production-quality code in accordance with company standards.


  • A Ph.D. in any related discipline in Life Sciences
  • One or more peer reviewed publications demonstrating proficiency in Structural Bioinformatics, such as a systematic analysis of PDB entries.
  • A general understanding of modern computational techniques in Structural Bioinformatics, including: denovo and template-based modeling of 3D structures, protein-ligand docking, protein-protein docking, molecular dynamics, coarse-grained simulations, structural alignments/superpositions, domain parsing techniques, secondary structure predictions/assignments, etc.
  • A general understanding of experimental and computational techniques for generating 3D models of proteins.
  • 2+ years experience with Python, including knowledge of best practices
  • Scientific programming experience, notably: numpy, scipy, scikit-learn, biopython
  • Experience developing code collaboratively
  • Experience with cloud computing and storage
  • A general understanding of SLDC standards and best practices
  • How to Apply

    Please email a resume to Applications will be accepted until the positions are filled. Local candidates preferred. Only successful applicants will be contacted. For more information about our company, please visit: