Scientist/Sr. Scientist, Computational Biophysics/Molecular Design

Boston, MA
May 09, 2022
Required Education
Position Type
Full time

Scorpion Therapeutics is a precision oncology company founded in February 2020 by a preeminent group of scientists from Harvard University/Massachusetts General Hospital – Keith Flaherty, MD, Gaddy Getz, Ph.D. and Liron Bar-Peled, Ph.D. The company has raised $270M in Series A and Series B financings led by blue-chip investors, including Atlas Venture, Boxer Capital of Tavistock Group, EcoR1 Capital, LLC, Omega Funds, and Vida Venture.

Scorpion Therapeutics’ mission is to serve oncology patients by discovering and developing best-in-class and first-in-class, small molecule cancer medicines that address large patient segments with significant unmet medical needs. To accomplish this mission, we are building a highly collaborative team focused on the pursuit of novel approaches to small molecule drug discovery. This approach relies upon dynamic collaboration between cancer biology, proteomics, informatics, structural biology and medicinal chemistry – with the ultimate goal of realizing the full potential of targeted/precision oncology.

Scientist/Sr. Scientist, Computational Biophysics/Molecular Design

Scorpion Therapeutics 

You’ll deploy in silico techniques to characterize protein dynamics of undruggable targets and identify potential binding sites, cryptic pockets, and allosteric mechanisms. You’re an integral member of cross-functional project teams to identify and characterize hits identified through our screening platform for targets of interest. You’ll drive insights from the integration of experimental, structural, and in silico data to enable efficient optimization from hit to lead. In addition, you’ll identify and incorporate novel approaches in collaboration with the data science team to further enhance our molecular design platform.


  • Provide integrated computational biophysics support to help drive understanding of protein-structure-function-dynamics relationships of novel targets, including allosteric regulation and occurrence of cryptic pockets
  • Integrate computational biophysics approaches like Markov State Modeling, metadynamics or other enhanced sampling techniques, and classical molecular dynamics into our drug discovery workflows
  • Develop approaches to identify and map novel binding sites for compound targeting
  • In collaboration with medicinal chemists deploy computational chemistry techniques to accelerate hit-to-lead design campaigns
  • Collaborate with experimental biophysicists and biochemists to design experiments to validate computational predictions
  • Collaborate with the Data Science team to develop and integrate data analytics approaches into the analysis of molecular simulations, including statistical and machine learning methods


  • Passionate about applying and developing computational methods to enable the discovery of novel medicines
  • PhD in computational biophysics/chemistry/physics or related fields with 4+ years of project support in a pharmaceutical and/or biotechnology environment
  • Extensive experience in developing analysis workflows for molecular simulation data, including but not limited to identification of cryptic pockets, characterization of induced fit effects, identification of allosteric regulation mechanisms
  • Demonstrated contributions to the advancement of drug discovery projects through the application of computational biophysics and chemistry techniques
  • Experience with Machine Learning approaches for molecular simulation analysis a plus
  • Demonstrated ability to program in Python or other languages. Familiarity with ML libraries
  • Experience with full Schrödinger software suite and AMBER a plus
  • You are a great communicator who enjoys working in a highly integrated, fast-moving biotech environment


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.