Postdoctoral Fellow in Computational Chemistry

Faculty/Division: Temerty Faculty of Medicine

Department: Structural Genomics Consortium

Campus: St. George (Downtown Toronto)

Supervisor: Pr. Matthieu Schapira, U. of Toronto

Co-Supervisor: Pr. John Irwin, UCSF


About us:

Home to over 40 departments and institutes, the University of Toronto's Temerty Faculty of Medicine lies at the heart of the Toronto Academic Health Science Network and is a global leader in ground-breaking research and education, spanning clinical medicine, basic science, and the rehabilitation sciences sectors.


The Structural Genomics Consortium (SGC) is an international Public-Private Partnership that supports the discovery of new medicines through open-access research ( Led from Toronto, the SGC within the Temerty Faculty of Medicine, University of Toronto is supported by public and philanthropic funding agencies and ten pharmaceutical industry partners. The SGC-Toronto Research Informatics group led by Dr. Matthieu Schapira is seeking an ambitious and scientifically creative Postdoctoral Research Fellow to computationally expand the accessible chemical space and harness novel applications in deep learning for drug discovery. The candidate will also analyze computational methods and experimental data from CACHE challenges led by Dr Schapira and publish annually the learnings on the state-of-the-art in computational hit finding. This position will be co-supervised by Dr. John Irwin, UCSF.

Responsibilities [33% effort each]:

1- Work with chemists across Canada to build and grow a pan-Canadian chemical library following the preliminary work described in and Dr. Irwin’s pioneering work described in

Analyze the drug-likeness, chemical diversity, and uniqueness of the library.

2- Identify, evaluate and use the best AI-accelerated open source and commercial software to screen this and other libraries:

  • conformers generation, tautomers prediction and virtual screening of ultra-large chemical libraries
  • synthon-based virtual screening
  • molecular dynamics simulations
  • free energy perturbation

and work in close collaboration with a multi-disciplinary team of co-funded chemists across Canada and, biophysicists, structural and cell biologists at the SGC lab who will experimentally test computational predictions to advance open science drug discovery projects.

3- Analyze and publish learnings from CACHE challenges:

  • Identify common and distinctive features in best-performing computational screening pipelines used by AI experts and leading computational chemists around the world
  • Evaluate the chemical novelty and drug-likeness of predicted hits
  • Delineate the evolving state-of-the-art in computational hit-finding
  • Publish learnings in annual CACHE papers (inaugural paper planned in Q4 2024 – see white paper for details)


Proficiency in Python, RDKit and installation/deployment of GitHub packages.

Proficiency in cheminformatics and the manipulation of ultra-large chemical libraries.

Experience with chemical library management in PostgreSQL is a plus.

Demonstrated experience in structure-based drug design, including hit discovery (virtual screening) and hit-to-lead optimization (MD, FEP).

Proficiency with at least one leading computational chemistry suite.

Strong English language, organizational, team, and communication skills.

Ph.D. obtained within the last 2 years. Please do not apply otherwise.

Interested candidates, please send a CV and cover letter to Dr. Matthieu Schapira with the subject line Postdoctoral Position in Computational Chemistry.

Diversity Statement:

The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from racialized persons/persons of colour, women, Indigenous / Aboriginal People of North America, persons with disabilities, LGBTQ2S+ persons, and others who may contribute to the further diversification of ideas.

Accessibility Statement:

The University strives to be an equitable and inclusive community and proactively seeks to increase diversity among its community members. Our values regarding equity and diversity are linked with our unwavering commitment to excellence in the pursuit of our academic mission.

The University is committed to the principles of the Accessibility for Ontarians with Disabilities Act (AODA). As such, we strive to make our recruitment, assessment and selection processes as accessible as possible and provide accommodations as required for applicants with disabilities.

If you require any accommodations at any point during the application and hiring process, please contact us at

The SGC as part of the Nuffield Department of Medicine is a family friendly department:

Closing Date: 
Friday 31st May 2024
glqxz9283 sfy39587stf02 mnesdcuix8