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Open Position

Director of Cheminformatics

Full-time role based in Boston, MA

Full-time role based in Boston, MA

Within every human cell, nature has engineered finely tuned control mechanisms to correct imbalances caused by stress and disease and promote healing. At HotSpot Therapeutics, nature is inspiring us to create a wave of new medicines.

Through a proprietary technology platform, we are uncovering privileged allosteric sites used by nature to control proteins – called regulatory hotspots– that can be exploited through small molecule drug discovery. Regulatory hotspots are allowing sought-after targets to be drugged for the first time while delivering molecules with exquisite selectivity and attractive drug-like properties.

HotSpot is supported by a syndicate of leading healthcare investors based in the US and Europe. You will be joining a seasoned team of drug hunters with an excellent track record in drug discovery.  As a HotSpotter, you are comfortable thinking outside the box and breaking convention. You are curious about the world and contribute beyond your precise role description. You are action orientated and extraordinary at getting things done. You communicate openly with your colleagues and you hate office politics.

HotSpot is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees.

Key Responsibilities:

  • Develop cheminformatics algorithms for drug discovery
  • Design and build toolkits for library design of over 20 million molecules
  • Lead the efforts to design DNA-encoded libraries specifically for regulatory hotspots
  • Apply your skills and experience to augment our proprietary platform
  • Develop advanced molecular design algorithms and visualization (like maximum common substructure search algorithms i.e., maximum clique problem)
  • Ability to develop novel AI algorithms and data analysis tools
  • Stay on top of latest developments in the field of machine learning cheminformatics and lead the internalization of promising approaches
  • Interact within a multidisciplinary team
  • Clearly communicate results and suggestions in written and oral form


  • M.S./Ph.D. in Computational Science (cheminformatics, computer science, computational chemistry/physics/biology or related discipline) with 10-12 years of experience
  • Experience in algorithms and methods development. GUI development is a plus, but not a requirement
  • Expert level experience with at least one scripting/programming and analytics language (Python, C++, R or similar)
  • Experience with cheminformatics applications (OEChem TK, RDkit etc) and pipelining workflow tools (Knime, Pipeline Pilot etc.)
  • Understanding of chemical and protein structures; Experience handling various file types/formats e.g., smiles, smarts, SDF, PDB, MOL2 etc.
  • Working experience with enumeration (reaction/Markush), breaking & reassembling millions of molecules in fractions of seconds using scripts
  • Knowledge of Oracle/chemical cartridge and SQL/PL
  • Solid statistics training and experience in advanced analytics and data science methods (random forest, clustering, neural networks and deep learning
  • Bayesian classifications, anomaly detection, dimensionality reduction and etc.)
  • Basic understanding of organic chemistry, understanding of medicinal chemistry a plus
  • Desire to learn and apply new techniques
  • Excellent communication skills


If your skills are a match for this opportunity, please email: