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Scientist I/II, Protein and Chemistry Machine Learning

Scorpion Therapeutics

Scorpion Therapeutics

Software Engineering
Boston, MA, USA
Posted on Thursday, May 9, 2024

Scorpion is a pioneering clinical-stage oncology company redefining the frontier of precision medicine to deliver optimized and transformational therapies for larger populations of patients with cancer. Scorpion has built a proprietary and fully integrated platform of the most advanced technologies across cancer biology, medicinal chemistry, and data sciences, with the goal of consistently and rapidly creating exquisitely selective small molecule compounds against an unprecedented spectrum of targets. Scorpion aims to leverage its platform to advance a broad pipeline of wholly owned, optimized compounds across three target categories: best-in-class molecules targeting validated oncogene targets; first-in-class molecules for previously undruggable targets; and first-in-class molecules for novel cancer targets.

We are seeking a highly motivated machine learning scientist to join the Chemical Data Science team. The Chemical Data Science team is tightly integrated with protein and structural sciences, medicinal chemistry, chemical proteomics, and plays an important role in drug discovery project teams. The successful candidate will be responsible for the development and implementation of data analytics and machine learning methods to enable target prioritization and drug discovery efforts.

Responsibilities can include

  • Development and implementation of advanced data analytics and state-of-the-art machine learning models to generate insights from proteomics (ABPP) data, protein structure, and protein dynamics to enhance target prioritization and structure-based drug design efforts
  • Development and validation of predictive models for GSH reactivity, cysteine reactivity, and ADME properties of small molecules
  • Deployment and fine-tuning of generative chemistry approaches
  • Be an integral, proactive member of a highly interdisciplinary team and drug discovery projects
  • Stay up-to-date with the latest advances in machine learning and drug discovery
  • Contribute to the development of our computational infrastructure by identification and incorporation of novel tools in collaboration with the Data Science and broader Scorpion team


  • PhD or MSc in computational biophysics, computational chemistry, chemical engineering, computer science, machine learning or related field
  • Extensive hands-on experience with ML methods in chemistry, and/or structural biology
  • Experience with data analytics approaches related to the large heterogeneous proteomics data sets
  • Strong scientific programming skills with Python
  • Experience with at least one open-source high-end development environment such as PyTorch or TensorFlow
  • Familiarity with code versioning tools (Git/GitHub)
  • Experience with RDKit, OEChem, Schrödinger, or other cheminformatics and computational chemistry toolkits
  • Experience with cloud computing infrastructures (AWS preferred)
  • Excellent problem-solving skills and ability to balance the tradeoffs between the speed and quality while working independently in a fast-paced, highly collaborative environment
  • Great communication skills, both written and verbal

Nice to have

  • Post-PhD/Msc work experience in an industry/biotech setting
  • Experience with development of data processing workflows and infrastructure
  • Practical experience developing deep generative methods in chemistry
  • Demonstrated experience developing software in a team setting
  • Familiarity with CICD and MLOps

Scorpion Therapeutics Inc. is an Equal Opportunity Employer who strives to create and maintain a diverse working environment. We do not discriminate for reasons of race, color, religion, gender, national origin, age, sexual orientation, marital or veteran status, disability, or any other legally protected status. Beginning October 13, 2021, Scorpion Therapeutics requires all new hires to be fully vaccinated against COVID-19. If you are unable to receive the vaccine due to a disability or serious medical condition, or because of your sincerely held religious beliefs, you will have an opportunity to request a reasonable accommodation.